Národní úložiště šedé literatury Nalezeno 10 záznamů.  Hledání trvalo 0.03 vteřin. 
Preparation of modified oligonucleotides by nicking enzyme amplification reaction
Ménová, Petra ; Hocek, Michal
A method for the enzymatic synthesis of short (10-22 nt) base-modified oligonucleotides was developed, based on the nicking enzyme amplification reaction. The methodology, including product isolation and purification, was scaled up to nanomolar amounts. The modified oligonucleotides were successfully used as primers in primer extension and PCR, affording primer-modified oligonucleotides and DNA. Two simple and efficient methods for fluorescent labelling of the PCR products were also developed.
Study of DNA-protein interactions by cross-link formation using aqueous Michael addition
Daďová, Jitka ; Orság, Petr ; Pohl, Radek ; Brázdová, Marie ; Fojta, Miroslav ; Hocek, Michal
Acrylamide and vinylsulfonamide were designed as reactive DNA modifications for covalent crosslinking with cysteine containing peptides and proteins. The corresponding functionalized cytidine triphosphates were prepared and enzymatically incorporated into DNA. These modified oligonucleotides were then used for conjugation with DNA binding domain of protein p53.
Polymerase synthesis of base-modified DNA: New methods and new applications
Balintová, Jana ; Daďová, Jitka ; Kielkowski, Pavel ; Ménová, Petra ; Vaníková, Zuzana ; Riedl, Jan ; Raindlová, Veronika ; Fojta, Miroslav ; Hocek, Michal
Diverse base-modified oligonucleotides and double-stranded DNA molecules were prepared by polymerase incorporation of modified nucleoside triphosphates. The methods include primer extension, PCR, nicking enzyme amplification reaction and mixed incorporations. The modified nucleic acids were used in redox and fluorescence labelling and coding, as well as regulation of binding and cross-linking with proteins.
Redox labelling of nucleic acids for analyzing nucleotide sequences and monitoring DNA-protein interactions
Fojta, Miroslav ; Havran, Luděk ; Horáková Brázdilová, Petra ; Pivoňková, Hana ; Kostečka, Pavel ; Macíčková-Cahová, Hana ; Raindlová, Veronika ; Vrábel, Milan ; Hocek, Michal
Nucleobase labelling of DNA for electrochemical sensing was attained through chemical modification of thymine bases with osmium tetroxide in the presence of nitrogenous ligands, or via enzymatic incorporation of nucleotide conjugates with redox-active moieties using labelled deoxynucleoside triphosphates. DNA hybridization, primer extension and PCR techniques were used for sequence-specific DNA assays. Tail-labelled DNA substrates were applied to monitor DNA binding by tumour suppressor p53 protein.
Direct enzymatic synthesis of aldehyde-functionalized DNA and its conjugation with hydrazines and amines
Raindlová, Veronika ; Hocek, Michal
A new simple methodology for DNA conjugation or staining was developed. 2′-Deoxyribonucleoside triphosphates (dNTPs) bearing reactive aldehyde group were prepared by one-step Suzuki cross-coupling reaction of halogenated dNTPs with boronic acid. These modified dNTPs were enzymatically incorporated into DNA by primer extension (PEX) or amplified by polymerase chain reaction (PCR) using different DNA polymerases. The followup reaction between aldehyde-modified PCR products and hydrazine derivatives gave coloured DNA conjugated hydrazones. This methodology was also used for further conjugations of aldehyde-modified 2′-deoxyribonucleoside monophosphates (dNMPs) with amines by reductive amination.
Polymerase synthesis of modified DNA containing cytosine in major groove
Kielkowski, Pavel ; Hocek, Michal
(Cytosine-5-yl)ethynyl derivatives of pyrimidine and 7-deazaadenine 2-deoxyribonucleosides and nucleoside triphosphates (dNTPs) were prepared by aqueous Sonogashira coupling. All modified dNTPs were excellent substrates for DNA polymerases to give DNA bearing acetylene- linked cytosine(s) in the major groove.
Synthesis of nucleotides bearing oligopyridine ligands and their incorporation into DNA
Kalachová, Lubica ; Hocek, Michal
The synthesis of 7-deaza-dATPs and dCTPs bearing bipyridine or terpyridine ligands via acetylene tethers was accomplished through Pd-catalyzed cross-coupling reactions. Different DNA polymerases were used for their incorporation into DNA.
Synthesis of nucleosides and nucleoside triphosphates bearing anthraquinone substituents as redox probes and their enzymatic incorporation to DNA
Balintová, Jana ; Havran, Luděk ; Fojta, Miroslav ; Hocek, Michal
Modified 2′-deoxynucleosides and nucleoside triphosphates (dNTPs) bearing anthraquinone (AQ) via acetylene or propargylcarbamoyl linkers were prepared by single-step Sonogashira cross-coupling reactions halogenated nucleosides (7-iodo-7-deaza-2′-deoxyadenosine and 5-iodo-2′-deoxycytidine) or dNTPs with N-(2-propynyl)-anthraquinone carboxamide and 2-ethynylantraquinone. Polymerase incorporation of the AQ-labelled dNTPs into DNA has also been studied. Square-wave voltammetry of the AQ-labelled nucleosides and nucleotides showed one reversible peak at –0.5 V.
Synthesis of biaryl-substituted fluorescent nucleosides and nucleoside triphosphates and their incorporation to DNA
Riedl, Jan ; Hocek, Michal
A series of modified nucleosides bearing the fluorescent substituted biaryl labels attached to nucleobase was prepared and their luminescent properties were evaluated. The modified nucleosides show divers fluorescence from 400 to 560 nm when excited at 340 nm in water depending on structural and substitution pattern. The corresponding biaryl-substituted nucleoside triphosphates (dNTPs) were prepared analogously and used for polymerase incorporation to DNA. Applications in hybridization probes were studied.
Polymerase construction of base-modified DNA for chemical biology
Hocek, Michal ; Macíčková-Cahová, Hana ; Kielkowski, Pavel ; Raindlová, Veronika ; Kalachová, Lubica ; Riedl, Jan ; Balintová, Jana ; Ménová, Petra
An efficient two-step methodology for construction of base-modified DNA was developed based on aqueous-phase cross-coupling reactions of halogenated nucleoside triphosphates (dNTPs) followed by polymerase incorporation. A number of diverse chemical modifications have been successfully incorporated in this way for the use in chemical biology (modulation of cleavage by restriction enzymes, interactions with diverse DNA-binding proteins and bioconjugations).

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