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New Ligands for Modification of DNA by Osmium Tetroxide Reagents
Havran, Luděk; Zenka, Martin; Fojta, Miroslav
2016 - English
Besides DNA intrinsic electroactivity, modification of DNA by redox active tags find wide use in electrochemical analysis of DNA interactions and damage. Application of these tags can improve specificity of the analysis. One from utilized labels in this field are complexes of osmium tetroxide with nitrogen ligands, which produce with DNA electroactive covalent adducts. These complexes preferentially react with thymine in single strand DNA. Type of used ligand influence electrochemical behavior forming adducts. In this contribution will be presented results which are acquired by testing of set a new ligands based of quinone and substituted 1, 10-phenanthroline.
Keywords:
nucleic-acids; complexes; dna; Osmium tetroxide complexes
Available at various institutes of the ASCR
New Ligands for Modification of DNA by Osmium Tetroxide Reagents
Besides DNA intrinsic electroactivity, modification of DNA by redox active tags find wide use in electrochemical analysis of DNA interactions and damage. Application of these tags can improve ...
Synthetic Biology Introduces New Base Pairs to Analyze
Špaček, Jan
2016 - English
An unnatural base pair is composed of two nucleobase analogues which specifically Pair only with each other similarly as natural DNA pairs do. Goal of the search for new base pair is expansion of genetic alphabet with new codons containing unnatural bases. Expanded genetic alphabet am, other things allows simultaneous site specific incorporation of non-standard amino acids into proteins Recently unnatural bases forming pairs vie hydrophobic interactions, which can be replicated by prokaryotic cells with efficiency and mutation rate similar to natural base pairs, have been shown. Synthetic biology provides new opportunities for application of electrochemical analysis.
Keywords:
expanded genetic alphabet; escherichia-coli; dna
Available at various institutes of the ASCR
Synthetic Biology Introduces New Base Pairs to Analyze
An unnatural base pair is composed of two nucleobase analogues which specifically Pair only with each other similarly as natural DNA pairs do. Goal of the search for new base pair is expansion of ...
Analysis of Denatured PCR Products Modified with 7-deazapurine Bases at Hanging Mercury Drop Electrode
Dudová, Zdenka; Špaček, Jan; Havran, Luděk; Pivoňková, Hana; Fojta, Miroslav
2016 - English
7-deazapunines are synthetic analogues of natural purine nucleobases which can pair with pyrimidines, retaining pairing complementarity of their parent purines. There is replaced N7 atom by CH group in 7-deazapurines so that DNA modified with them don't participate in Hoogsteen basepairing and don't form alternative structures. Here is a study of 7-deazapurines incorpotated into DNA measured at HMDE by CV and ACV. While 7-deazaadenine was reduced at the HMDE, giving rise to a similar irreversible cathodic peak as the natural adenine, 7-deazaguanine didn't yield any peak analogous to the peak G due to Guanine, in Agreement with a loss of corresponding redox in 7-deazaguanine.
Keywords:
dna; pcr; hmde; Voltammetry
Available at various institutes of the ASCR
Analysis of Denatured PCR Products Modified with 7-deazapurine Bases at Hanging Mercury Drop Electrode
7-deazapunines are synthetic analogues of natural purine nucleobases which can pair with pyrimidines, retaining pairing complementarity of their parent purines. There is replaced N7 atom by CH group ...
Electrochemical Analysis of Carrageenans. The Effect of Acetate Concentration
Kos, S.S.; Paleček, Emil
2016 - English
kappa-, iota-, and lambda-carrageenans are polysaccharides (PSs) which produce electrocatalytic chronopotentiometric peak H-ps in acetate buffer (pH 5.2) on the hanging mercury drop electrode (HMDE). Here we show that this peak (E-p1.8V) increases with the acetate concentration Using a. c. voltammetry we found that the appearance and the observed increase of peak H-PS is accompanied by a decrease of capacitive current below the background elecnolyte around1.8 V, suggesting strong adsorption of the negatively charged PS at the negatively charged HMDE. Compared to carrageenany dextran did not produce peak H-PS and did not strongly adsorb at negatively charged electrode.
Keywords:
polysaccharides; carageenans; chronopotentiometry; peak H-ps
Available at various institutes of the ASCR
Electrochemical Analysis of Carrageenans. The Effect of Acetate Concentration
kappa-, iota-, and lambda-carrageenans are polysaccharides (PSs) which produce electrocatalytic chronopotentiometric peak H-ps in acetate buffer (pH 5.2) on the hanging mercury drop electrode (HMDE). ...
Electrochemical Analysis of Chemically Modified DNA at Gold Electrodes
Vidláková, Pavlína; Havran, Luděk; Fojta, Miroslav
2016 - English
DNA labeling is used to increase sensitivity of its electrochemical detection. Covalently bound markers based on a complex of osmium tetroxide with 22-bipyridine(Os,bipy) is one of those frequently applied. Os bipy reacts with pyrimidines (mainly thymines) in single stranded regions of DNA, therefore it represents a useful marker for the analysis of DNA structure or labeling of hybridization probes . Another possibility of DNA labeling is the incorporation of chemically modified dNTPs into DNA molecules with using primer extension. DNA labeling in connection with voltammetry at gold electrodes has application potential in development of sensors for studying of DNA structure and interaction.
Keywords:
enzymatic incorporation; nucleic-acids; immobilization
Available at various institutes of the ASCR
Electrochemical Analysis of Chemically Modified DNA at Gold Electrodes
DNA labeling is used to increase sensitivity of its electrochemical detection. Covalently bound markers based on a complex of osmium tetroxide with 22-bipyridine(Os,bipy) is one of those frequently ...
Label-free Detection of Single Nucleotide Polymorphism Using Selective Incorporation of Biotin Anchor and Magnetoseperation on Streptavidin Magnetic Beads
Plucnara, Medard; Havran, Luděk; Ecsin, E.; Erdem, A.; Fojta, Miroslav
2016 - English
Novel approach of SNP detection in model synthetic oligonucleotides is described.This assay requires only intrinsic electrochemical properties of DNA and except of incorporation of biotin affinity tag, no any labeling or any other modification step is needed. Very good resolution for different variants of polymorphism as well as sufficiently low detection limits were achieved.In combination with using pencil graphited electrode this assay could be very simple and cheap tool for SNP typing.
Keywords:
surface-plasmon resonance; copper ions; Label-free detection
Available at various institutes of the ASCR
Label-free Detection of Single Nucleotide Polymorphism Using Selective Incorporation of Biotin Anchor and Magnetoseperation on Streptavidin Magnetic Beads
Novel approach of SNP detection in model synthetic oligonucleotides is described.This assay requires only intrinsic electrochemical properties of DNA and except of incorporation of biotin affinity ...
Primer Extension Reaction at the Gold Electrode Surface
Vidláková, Pavlína; Havran, Luděk; Fojta, Miroslav
2015 - English
One option of covalent DNA labeling is incorporation of chemically modified nucleotides using corresponding deoxynucleotide triphosphates into DNA molecules using polymerase-catalyzed primer extension. Primer extension is usually performed in solution and then the product is analyzed, often after a suitable separation. In our study we tested the possibility to prepare oligonucleotides with enzymatically incorporated anthraquinone labeled nucleotides using primer extension on templates immobilize at a gold electrode surface.
Keywords:
dna; immobilization; optimization
Available at various institutes of the ASCR
Primer Extension Reaction at the Gold Electrode Surface
One option of covalent DNA labeling is incorporation of chemically modified nucleotides using corresponding deoxynucleotide triphosphates into DNA molecules using polymerase-catalyzed primer ...
Natural and Synthetic Components of Nucleic Acids as Reactive Sites for DNA Modification by Osmium Tetroxide Complexes
Havran, Luděk; Špaček, Jan; Rozkosna, Jana; Fojta, Miroslav
2015 - English
Natural DNA electroactivity find wide use in electrochemical analysis of its interactions and damage. For some applications is useful applied redox active tag to improve specificity of the analysis. One from utilized labels in this field are complexes of osmium tetroxide with nitrogen ligands (Os, L), which produce with DNA electroactive covalent adducts. Prime reaction site for Os, L is C=C double bond in pyrimidine nucleobases. If is 2,2'-bipyridine used as ligand, reaction is specific for single strand DNA. In this contribution will be presented results of electrochemical analysis of Os, bipy adducts with different ODN containing chemically modified purine bases.
Keywords:
dna; Osmium tetroxide complexes; Electrochemical methods
Available at various institutes of the ASCR
Natural and Synthetic Components of Nucleic Acids as Reactive Sites for DNA Modification by Osmium Tetroxide Complexes
Natural DNA electroactivity find wide use in electrochemical analysis of its interactions and damage. For some applications is useful applied redox active tag to improve specificity of the analysis. ...
Studies of Protein-DNA Interactions using Immunoprecipitation with DNA Probes Labelled with Electroactive Groups
Hermanová, Monika; Špaček, Jan; Pivoňková, Hana; Fojta, Miroslav
2015 - English
Different electrochemically active species were tested for labelling of DNA probes and detection of DNA-protein binding. As the DNA probes, oligonucleotides bearing or lacking specific binding site of the p53 protein were chosen. They were tail-labelled either via chemical modification of single-stranded (ss) oligo(dT) DNA tails with an oxoosmium complex, or via enzymatic synthesis of the ss tail by terminal deoxynucleotidyl transferase and deoxynucleoside triphosphates modified with electrochemically reducible moieties. Electrochemical detection enabled to discriminate between sequence-specific and non-specific p53-DNA binding.
Keywords:
electrochemical detection; Protein-DNA binding; p53
Available at various institutes of the ASCR
Studies of Protein-DNA Interactions using Immunoprecipitation with DNA Probes Labelled with Electroactive Groups
Different electrochemically active species were tested for labelling of DNA probes and detection of DNA-protein binding. As the DNA probes, oligonucleotides bearing or lacking specific binding site of ...
Study on the Electrophoretic Behaviour of Short Oligodeoxyribonucleotides in Fused Silica Capillaries. A Preliminary Communication
Vítová, Lada; Fojta, Miroslav; Vespalec, Radim
2015 - English
Effects of background electrolyte pH, composition and concentration on the electrophoretic transport of short oligodeoxyribonucleotides (ODNs) in fused silica capillaries have been investigated in the presented study. Mobilities and separation efficiencies of ODNs peaks varied with all three background electrolyte characteristics. Just changes in the background electrolyte characteristics and acid-base properties of ODNs are not sufficient for a systematic explanation of the observed variations. Despite the indicated complexity of ODNs electrophoretic behaviour, we show that very high separation efficiencies of ODNs peaks can be achieved in background electrolytes of physiological pH.
Keywords:
separation; oligonucleotides; nucleotides; capillary electrophoresis
Available at various institutes of the ASCR
Study on the Electrophoretic Behaviour of Short Oligodeoxyribonucleotides in Fused Silica Capillaries. A Preliminary Communication
Effects of background electrolyte pH, composition and concentration on the electrophoretic transport of short oligodeoxyribonucleotides (ODNs) in fused silica capillaries have been investigated in the ...
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