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New oxidative labels for electrochemical detection of DNA
Simonova, Anna; Havran, Luděk; Fojta, Miroslav; Hocek, Michal
2014 - English
New dCTP and dATP derivatives bearing oxidizable labels have been synthesized and incorporated to DNA for studying their electrochemical properties in different sequences of DNA.
Keywords:
dNTPs; DNA; electrochemical properties
Available at various institutes of the ASCR
New oxidative labels for electrochemical detection of DNA
New dCTP and dATP derivatives bearing oxidizable labels have been synthesized and incorporated to DNA for studying their electrochemical properties in different sequences of DNA.
Acyclic nucleoside bis-phosphonates as potent inhibitors of 6-oxopurine phosphoribosyltransferases
Špaček, Petr; Keough, D. T.; Vrbková, Silvie; Slavětínská, Lenka; Janeba, Zlatko; Naesens, L.; Edstein, M. D.; Chavchich, M.; Wang, T. H.; de Jersey, J.; Guddat, L. W.; Hocková, Dana
2014 - English
Hypoxanthine-guanin-(xanthine) phosphoribosyltransferase (HG(X)PRT) is critical for the survival of malarial parasites Plasmodium falciparum and Plasmodium vivax. These parasites rely on HG(X)PRT to make 6-oxopurine nucleoside monophosphates. Specific acyclic nucleoside phosphonates (ANPs) inhibit HG(X)PRT and thus have an anti-plasmodial activity. Crystal structures of human HGPRT in complex with several ANP-based inhibitors suggested that attachment of the second phosphonate group which could occupy the pyrophosphate binding site may lead to increased affinity of these compounds.
Keywords:
nucleotide analogues; enzyme inhibitors; Plasmodium
Available at various institutes of the ASCR
Acyclic nucleoside bis-phosphonates as potent inhibitors of 6-oxopurine phosphoribosyltransferases
Hypoxanthine-guanin-(xanthine) phosphoribosyltransferase (HG(X)PRT) is critical for the survival of malarial parasites Plasmodium falciparum and Plasmodium vivax. These parasites rely on HG(X)PRT to ...
Utilisation of enzymatic labelling with 4-aminophtalimide and 4-hydroxybenzylideneimidazolinone fluorescent derivates for monitoring of DNA-protein interaction
Orság, Petr; Pivoňková, Hana; Riedl, Jan; Hocek, Michal; Fojta, Miroslav
2014 - English
The 5’-substituted deoxycytosine triphosphates with conjugated solvatochromic derivates of 4-aminophtalimide (API) and derivates of the green fluorescent protein, 4-hydroxybenzylideneimidazolinone (HBI) were synthetized and successfully tested for enzymatic incorporation using primer extension assay. Site specifically labelled oligonucleotide probes were prepared and tested for interaction with p53 and SSB proteins, displaying distinct DNA-binding properties. The incorporation of multiple fluorescent labels did not interfere with natural protein binding and protein interaction leaded in both cases the to the gradual ratiometric increase of the fluorescence intensity moreover accompanied with the changes of the fluorescence emission spectra profile. Neither effect was observed after incubation with BSA, non-DNA binding protein, confirming the specificity of the interaction. Modified nucleoside triphosphates with conjugated fluorescence labels derivates of API and HBI can be used as substrates for preparation of the specific oligonucleotide labelled probes and provide the novel tool for studying and monitoring the DNA-protein interaction.
Keywords:
DNA-protein interaction; API; HBI
Available at various institutes of the ASCR
Utilisation of enzymatic labelling with 4-aminophtalimide and 4-hydroxybenzylideneimidazolinone fluorescent derivates for monitoring of DNA-protein interaction
The 5’-substituted deoxycytosine triphosphates with conjugated solvatochromic derivates of 4-aminophtalimide (API) and derivates of the green fluorescent protein, 4-hydroxybenzylideneimidazolinone ...
Searching for Electrochemical Reduction Mechanism of Azidophenyl DNA Labels
Daňhel, Aleš; Trošanová, Zuzana; Balintová, Jana; Hocek, Michal; Fojta, Miroslav
2014 - English
This contribution brings new information to sporadic scientific results concerned to electrochemical reduction of aromatic azides. Selected compounds used as perspective DNA labels or their structural constituents such as, 4-azidophenyltrifluoroboronic acid, 4-azidophenyl modified deoxycytidine and next probable analogous compounds and/or products of their reduction, were voltammetrically studied and compared to each other in order to reveal a mechanism of their electrochemical reduction at mercury electrodes in aqueous media. Preliminary results obtained by cyclic voltammetry at mercury and carbon based electrodes and by mass spectrometry of the products isolated from batch electrolysis on mercury pool by preparative chromatography are discussed.
Keywords:
aromatic azides; DNA labels; mercury electrode; reduction mechanism; voltammetry
Available at various institutes of the ASCR
Searching for Electrochemical Reduction Mechanism of Azidophenyl DNA Labels
This contribution brings new information to sporadic scientific results concerned to electrochemical reduction of aromatic azides. Selected compounds used as perspective DNA labels or their structural ...
Sulfur-containing phosphonate monomers for oligonucleotide synthesis
Kostov, Ondřej; Zborníková, Eva; Buděšínský, Miloš; Novák, Pavel; Rosenberg, Ivan
2014 - English
A series of novel compounds, protected S-MOP nucleoside-5’-O-methylphosphonothioates, was prepared as monomers for solid phase synthesis of phosphonothioate oligonucleotides. In addition we have examined the synthetic potential of nucleoside-5’-O-methyl-(H)-phosphinates for phosphonate oligonucleotide assembly.
Keywords:
S-MOP; oligonucleotides
Available at various institutes of the ASCR
Sulfur-containing phosphonate monomers for oligonucleotide synthesis
A series of novel compounds, protected S-MOP nucleoside-5’-O-methylphosphonothioates, was prepared as monomers for solid phase synthesis of phosphonothioate oligonucleotides. In addition we have ...
Vinyl-modified DNA and its cleavage by restriction endonucleases
Mačková, Michaela; Hocek, Michal
2014 - English
Three types of vinyl modified nucleoside triphosphates (dNVTPs) were prepared by single step aqueous Suzuki- Miyaura cross-coupling reaction of halogenated 2’-deoxynucleotides with vinyltrifluoroborate. These dNVTPs were enzymatically incorporated into DNA in Primer extension experiments and Polymerase chain reaction. Primer extension products were then tested for cleavage by series of type II restriction enzymes and the results were compared with a cleavage of ethynyl-modified DNA.
Keywords:
dNVTPs; DNA; cross-coupling reaction
Available at various institutes of the ASCR
Vinyl-modified DNA and its cleavage by restriction endonucleases
Three types of vinyl modified nucleoside triphosphates (dNVTPs) were prepared by single step aqueous Suzuki- Miyaura cross-coupling reaction of halogenated 2’-deoxynucleotides with ...
Enzymatic decomposition of a locked nucleoside phosphoramidate monitored by 31P NMR spectroscopy
Procházková, Eliška; Hřebabecký, Hubert; Nencka, Radim; Dračínský, Martin
2014 - English
Phosphoramidate derivatives are often used as prodrugs of modified nucleosides. The crucial step for the biologically active compound release in cells is then enzymatic hydrolysis of the phosphoramidate derivative. The enzymatic decomposition of a nucleoside prodrug 1 was monitored using 31P NMR spectroscopy and the structure of the reaction products was determined by 1D and 2D (COSY, HSQC, HMBC) NMR experiments and compared with the products obtained with non-enzymatic hydrolysis of the prodrug.
Keywords:
phosphoramidate derivatives; enzymatic hydrolysis; NMR spectroscopy
Available at various institutes of the ASCR
Enzymatic decomposition of a locked nucleoside phosphoramidate monitored by 31P NMR spectroscopy
Phosphoramidate derivatives are often used as prodrugs of modified nucleosides. The crucial step for the biologically active compound release in cells is then enzymatic hydrolysis of the ...
Novel conformationally locked nucleosides and nucleotides based on bicyclo[3.2.1]octane scaffold as a pseudosugar moiety
Šála, Michal; Dejmek, Milan; Procházková, Eliška; Hřebabecký, Hubert; Rybáček, Jiří; Dračínský, Martin; Novák, Pavel; Rosenbergová, Šárka; Fukal, J.; Sychrovský, Vladimír; Rosenberg, Ivan; Nencka, Radim
2014 - English
A route to a series of novel carbocyclic nucleosides locked in North conformation with bicyclo[3.2.1]octane scaffold was developed. Prepared nucleosides served as a starting material for the synthesis of modified oligomers [d(GCATATCAC), r(GCAUAUCAC), and A9]. Biological effects of the prepared nucleosides as well as the hybridization properties of the appropriate duplexes were evaluated.
Keywords:
locked nucleosides; LNA
Available at various institutes of the ASCR
Novel conformationally locked nucleosides and nucleotides based on bicyclo[3.2.1]octane scaffold as a pseudosugar moiety
A route to a series of novel carbocyclic nucleosides locked in North conformation with bicyclo[3.2.1]octane scaffold was developed. Prepared nucleosides served as a starting material for the ...
Bi-substrate inhobitors of human pyrimidine 5’-nucleosidases
Šimák, Ondřej; Pachl, Petr; Jandušík, T.; Brynda, Jiří; Buděšínský, Miloš; Rosenberg, Ivan
2014 - English
The work is aimed at the synthesis of bi-substrate inhibitors of 5’-nucleosidases. The pyrimidine nucleobase of lead compound was derivatized in the 5-position with various phosphonic acids differing in conformational flexibility and in the length of alkyl side chain carrying phosphonate group. The phosphonic acid with optimal linker can reach the phosphate binding side and make strong interaction with the enzyme. Inhibition activity of such inhibitors and crystal structure of inhibitor-enzyme complex will be presented.
Keywords:
5’-nucleosidases; NPAs; bi-substrate inhibitors
Available at various institutes of the ASCR
Bi-substrate inhobitors of human pyrimidine 5’-nucleosidases
The work is aimed at the synthesis of bi-substrate inhibitors of 5’-nucleosidases. The pyrimidine nucleobase of lead compound was derivatized in the 5-position with various phosphonic acids differing ...
Synthesis and biological activity of thiophene fused 7-deazapurine ribonucleosides
Tichý, Michal; Hocek, Michal
2014 - English
A series of thieno[2’,3’:4,5]pyrrolo[2,3-d]pyrimidine ribonucleosides bearing various alkyl, amino or hetaryl groups in position 4 has been prepared and all compounds have been tested for cytostatic and antiviral activities (HCV and Dengue viruses).
Keywords:
nucleosides; cytostatics; 7-deazapurine ribonucleosides
Available at various institutes of the ASCR
Synthesis and biological activity of thiophene fused 7-deazapurine ribonucleosides
A series of thieno[2’,3’:4,5]pyrrolo[2,3-d]pyrimidine ribonucleosides bearing various alkyl, amino or hetaryl groups in position 4 has been prepared and all compounds have been tested for cytostatic ...
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