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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.
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Tail labelled oligonucleotide probes for the detection of DNA-protein interactions
Pivoňková, Hana ; Němcová, Kateřina ; Horáková Brázdilová, Petra ; Havran, Luděk ; Macíčková-Cahová, Hana ; Hocek, Michal ; Fojta, Miroslav
DNA-protein interactions can be monitored via different ways. We introduce novel, fast and simple approaches in DNA-protein interaction detection based on electrochemical measurements of DNA alone (structure-sensitive DNA sensing), or DNA modified with osmium tetroxide bearing nitrogenous ligands, or measurements of redox-active moieties enzymatically attached to the end of a DNA substrate thus forming a labeled tail (by terminal transferase).
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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.
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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.
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Dichotomy in regioselectivity of Pd-catalyzed direct C-H arylation of protected uracils
Čerňová, Miroslava ; Hocek, Michal
Uracil bases and nucleosides bearing aryl groups in positions 5 or 6 are an important class of compounds and display wide range of biological activities1. In addition, arylation in position 5 is often used for labeling of nucleotides, oligonucleotides and DNA for applications in bioanalysis or chemical biology2. The 5- or 6-aryluracils can be prepared by heterocyclization or by cross-coupling reactions of halouracils with arylboronic acids or stannanes or metallated uracils with aryl halides. Direct C–H arylation of uracil is an alternative to classical cross-couplings where the preparation of reactive organometallic reagent is avoided. Recently, we have developed regioselective Pd-catalyzed and/or Cu-mediated direct C–H arylations of 1,3-dimethyluracil as a model compound for pyrimidine bases to position C-5 or C-6 3.
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Modular synthesis of 5-substituted thiophene and furan C-nucleosides and their analogues
Bárta, Jan ; Hocek, Michal
A new modular and efficient methodology for the preparation of 5-substituted thiophen-2-yl and 5-substituted furan-2-yl C-nucleosides was developed. A Friedel–Crafts-type of C-glycosidation of 2-bromothiophene or 2-bromofuran with bis-toluoyl protected methyl- 2′-deoxyribofuranoside in presence of Lewis acid gave the desired bis-toluoyl protected 5-bromothiophne and 5-bromofuran C-nucleosides in good yields. They were used as key intermediates for Stille or Suzuki coupling whith (hetero)arylstannanes or boronic acids to afford a series of 5-(hetero)aryl thiophene and 5-(heteroaryl)furan C-nucleosides.
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