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Redox labeling and redox coding of nucleic acids
Balintová, Jana; Brázdová, Marie; Havran, Luděk; Fojta, Miroslav; Hocek, Michal
2014 - English
Modified nucleoside triphosphates (dNTPs) bearing benzofurazane, azides and triazoles were prepared by Sonogashira or Suzuki cross-coupling. Polymerase incorporations of the functionalyzed dNTPs into DNA by primer extension and their electrochemical properties have been studied.
Keywords:
nucleic acids; DNA; dNTPs
Available at various institutes of the ASCR
Redox labeling and redox coding of nucleic acids
Modified nucleoside triphosphates (dNTPs) bearing benzofurazane, azides and triazoles were prepared by Sonogashira or Suzuki cross-coupling. Polymerase incorporations of the functionalyzed dNTPs into ...
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
2014 - English
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.
Keywords:
nucleic acids; DNA; Michael addition
Available at various institutes of the ASCR
Study of DNA-protein interactions by cross-link formation using aqueous Michael addition
Acrylamide and vinylsulfonamide were designed as reactive DNA modifications for covalent crosslinking with cysteine containing peptides and proteins. The corresponding functionalized cytidine ...
Synthesis and biological properties of polysubstituted 5-nitrosopyrimidines
Janeba, Zlatko; Čechová, Lucie; Žurek, Jiří; Procházková, Eliška; Dračínský, Martin
2014 - English
2,4,6-Triamino-5-nitrosopyrimidines have been reported to contain a strong intramolecular hydrogen bond between the 5-nitroso and 4- or 6-amino groups, thus forming an additional pseudoring. Such analogues were speculated to be good mimics of fused bicyclic derivatives, e.g. purines. A series of novel polysubstituted 2-amino-5-nitrosopyrimidines, as potential structural mimics of modifi ed purine nucleos(t)ides well-known for their important biological properties, has been designed and synthesized. The physicochemical and biological properties of the prepared polysubstituted 2-amino-5-nitrosopyrimidines are being evaluated.
Keywords:
polysubstituted 5-nitrosopyrimidines; intramolecular hydrogen bond; NMR spectroscopy
Available at various institutes of the ASCR
Synthesis and biological properties of polysubstituted 5-nitrosopyrimidines
2,4,6-Triamino-5-nitrosopyrimidines have been reported to contain a strong intramolecular hydrogen bond between the 5-nitroso and 4- or 6-amino groups, thus forming an additional pseudoring. Such ...
Competitive incorporations of modified versus natural nucleotides by DNA polymerases
Kielkowski, Pavel; Hocek, Michal
2014 - English
A series of 7-substituted 7-deazaadenosine and 5-substituted cytosine triphosphates were tested in competitive incorporations with different DNA polymerases with their natural analogs and analyzed using restriction endonucleases and compared with steady state kinetics of the modified and natural dNTPs. Data sets correlation is up to 99 % and gave us to find modified dATPs with high incorporation ratios.
Keywords:
DNA polymerases; dNTPs
Available at various institutes of the ASCR
Competitive incorporations of modified versus natural nucleotides by DNA polymerases
A series of 7-substituted 7-deazaadenosine and 5-substituted cytosine triphosphates were tested in competitive incorporations with different DNA polymerases with their natural analogs and analyzed ...
Phosphanucleosides containing 1-hydroxymethylphospholane 1-oxide ring
Páv, Ondřej; Zborníková, Eva; Buděšínský, Miloš; Rosenberg, Ivan
2014 - English
Novel phosphanucleosides containing 1-hydroxymethylphospholane 1-oxide ring were synthesized as compounds with potential biological activity. A ring-closing metathesis was employed to prepare a phospholene precursor, which was then converted into either 4-azido-3-hydroxy-1-hydroxymethylphospholane 1-oxide or 3-azido-1- hydroxymethylphospholane 1-oxide derivatives. Subsequently, nucleobase was introduced using a nucleobase construction. The biological activity of prepared compounds was evaluated.
Keywords:
phosphanucleosides; 1-hydroxymethylphospholane 1-oxide ring; biological activity
Available at various institutes of the ASCR
Phosphanucleosides containing 1-hydroxymethylphospholane 1-oxide ring
Novel phosphanucleosides containing 1-hydroxymethylphospholane 1-oxide ring were synthesized as compounds with potential biological activity. A ring-closing metathesis was employed to prepare a ...
Activation of human RNase L by 5’-C-phosphonate-modified oligoadenylates
Petrová, Magdalena; Buděšínský, Miloš; Zborníková, Eva; Panova, Natalya; Novák, Pavel; Rosenberg, Ivan
2014 - English
Adeno’sine 5’-(S)-C-phosphonate (pCOHX) was prepared as monomer suitable for oligonucleotide synthesis. Modified tetramers pCOHXAAA and pCOHXAApCOHX were assembled on solid phase and evaluated for their ability to activate human RNase L.
Keywords:
human RNase L; oligoadenylates
Available at various institutes of the ASCR
Activation of human RNase L by 5’-C-phosphonate-modified oligoadenylates
Adeno’sine 5’-(S)-C-phosphonate (pCOHX) was prepared as monomer suitable for oligonucleotide synthesis. Modified tetramers pCOHXAAA and pCOHXAApCOHX were assembled on solid phase and evaluated for ...
Pyrrolidine nucleotides conformationally constrained via hydrogen bonding
Pohl, Radek; Poštová Slavětínská, Lenka; Rejman, Dominik
2014 - English
Conformation of pyrroPME nucleotide analogues was studied by means of NMR at different pD values in D2O solutions. Surprisingly, two stable conformers were found at pD > 9 for both cis and trans configurations and their ratio depended on the acid-base properties of nucleobase attached to pyrrolidine ring. The results of conformational analysis suggest that the conformation of the pyrrolidine ring is locked via intramolecular hydrogen bond between negatively charged phosphonate oxygen atom and protonized pyrrolidine nitrogen.
Keywords:
pyrrolidine nucleotides; PMEA; hydrogen bond
Available at various institutes of the ASCR
Pyrrolidine nucleotides conformationally constrained via hydrogen bonding
Conformation of pyrroPME nucleotide analogues was studied by means of NMR at different pD values in D2O solutions. Surprisingly, two stable conformers were found at pD > 9 for both cis and trans ...
Conformation analysis of nucleoside analogues containing selenium and tellurium in five-membered pseudosugar ring
Poštová Slavětínská, Lenka; Pohl, Radek; Rejman, Dominik
2014 - English
The conformation analysis of synthetized thymine and adenosine nucleoside analogues with selenium and tellurium in five-membered pseudosugar ring has been studied. The experimental NMR measurement was complemented with DFT molecular modeling studies. It was found, that ratio between individual conformers in solution depends on the nature of the heteroatom in the five-membered pseudosugar ring.
Keywords:
nucleoside analogues; five-membered pseudosugar ring; NMR
Available at various institutes of the ASCR
Conformation analysis of nucleoside analogues containing selenium and tellurium in five-membered pseudosugar ring
The conformation analysis of synthetized thymine and adenosine nucleoside analogues with selenium and tellurium in five-membered pseudosugar ring has been studied. The experimental NMR measurement was ...
Polymerase synthesis of new photocaged DNA
Vaníková, Zuzana; Hocek, Michal
2014 - English
5-[(2-nitrobenzyl)oxymethyl]-2’-deoxyuridine 5’-O-triphosphate (dUNBTP) and 5-hydroxymethyl-2’- deoxyuridine 5’-O-triphosphate (dUHMTP) were incorporated to diverse DNA sequences by polymerase synthesis (PEX or PCR). UHM modified DNA was synthesized also through the photolysis of photocaged, UNB-linked DNA. The presence of bulky NB-modification in the recognition sequence of DNA resulted in blocking of cleavage by all restriction endonucleases (REs), however sequences with small HM-modification (formed after irradiation by UV) were perfectly cleaved by all enzymes. Using of photoremovable protecting group in the DNA sequence presents bioorthogonal chemical masking and it has a potential in gene manipulation and cloning.
Keywords:
DNA; polymerase synthesis
Available at various institutes of the ASCR
Polymerase synthesis of new photocaged DNA
5-[(2-nitrobenzyl)oxymethyl]-2’-deoxyuridine 5’-O-triphosphate (dUNBTP) and 5-hydroxymethyl-2’- deoxyuridine 5’-O-triphosphate (dUHMTP) were incorporated to diverse DNA sequences by polymerase ...
Electrochemical analysis of DNA using switchable redox moieties
Fojta, Miroslav; Daňhel, Aleš; Horáková Brázdilová, Petra; Plucnara, Medard; Pivoňková, Hana; Havran, Luděk; Vidláková, Pavlína; Raindlová, Veronika; Balintová, Jana; Macíčková-Cahová, Hana; Hocek, Michal
2014 - English
Labelling of DNA with electrochemically active moieties proved to be a convenient way to the development of electrochemical techniques for the sequence-specific DNA sensing. Through combinations of various labels differing in redox potentials, independent redox coding of different DNA sequences or individual nucleobases can be attained. Applications possibilities of electrochemistry in analysis of modified DNAs are further extended by facile monitoring of chemical conversion of reactive groups on DNA during post-labelling with ultimate redox labels. In addition, controlled in situ electrochemical conversions of specific intrinsic and extrinsic DNA components can be utilized to switch their electrochemical signals and improve signal resolution.
Keywords:
DNA; electrochemical analysis; switchable redox moieties
Available at various institutes of the ASCR
Electrochemical analysis of DNA using switchable redox moieties
Labelling of DNA with electrochemically active moieties proved to be a convenient way to the development of electrochemical techniques for the sequence-specific DNA sensing. Through combinations of ...
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