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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 ...
Study of DNA oligonucleotides interactions with ethidium bromide by partial-filling affinity capillary electrophoresis
Růžička, Martin; Koval, Dušan; Kašička, Václav
2014 - English
A partial filling affinity capillary electrophoresis was developed and applied to investigation of non-covalent molecular interactions between double stranded DNA oligonucleotide (Dickerson dodecamer) and classical DNA intercalator ligand –ethidium bromide (EtBr). Binding constants of DNA EtBr complexes were determined from the dependence of migration time changes of DNA oligomer (applied as analyte) on the length of ligand zones introduced beforehand as plugs of various lengths in hydroxypropylcellulose coated fused silica capillary. Binding constants of DNA-EtBr complex were found to be in the range 4.2 x 103 – 1.5 104 L/mol.
Keywords:
affinity capillary electrophoresis; binding constant; oligonucleotide
Available at various institutes of the ASCR
Study of DNA oligonucleotides interactions with ethidium bromide by partial-filling affinity capillary electrophoresis
A partial filling affinity capillary electrophoresis was developed and applied to investigation of non-covalent molecular interactions between double stranded DNA oligonucleotide (Dickerson dodecamer) ...
Determination of enantiopurity of new types of acyclic nucleoside phosphonates by capillary electrophoresis with cyclodextrins-based chiral selectors
Šolínová, Veronika; Kaiser, Martin Maxmilian; Lukáč, Miloš; Janeba, Zlatko; Kašička, Václav
2014 - English
Capillary electrophoresis with neutral and cationic cyclodextrins as chiral selectors was applied for determination of enantiopurity analysis of new types of six acyclic nucleoside phosphonates, nucleotide analogues bearing ((3-hydroxypropan-2-yl)-1H-1,2,3-triazol-4-yl)phosphonic acid, 2-((diisopropoxyphosphonyl)methoxy)propanoic acid or 2 (phosphonomethoxy)propanoic acid moieties attached to adenine, guanine, 2,6-diaminopurine, uracil and 5-bromouracil nucleobases. All these compounds were found to be synthesized in pure enantiomeric forms. Employing the UV-absorption detection at 206 nm, their detection limits were in the low micromolar level.
Keywords:
acyclic nucleoside phosphonates; capillary electrophoresis; enantiopurity analysis
Available at various institutes of the ASCR
Determination of enantiopurity of new types of acyclic nucleoside phosphonates by capillary electrophoresis with cyclodextrins-based chiral selectors
Capillary electrophoresis with neutral and cationic cyclodextrins as chiral selectors was applied for determination of enantiopurity analysis of new types of six acyclic nucleoside phosphonates, ...
Novel conformationally locked nucleosides and nucleotides
Nencka, Radim; Šála, Michal; Hřebabecký, Hubert; Procházková, Eliška; Mackman, R.; Barauskas, O.; Lee, Y. J.; Tian, Y.
2014 - English
We report on a synthesis of two novel types of conformationally locked nucleoside analogues. We prepared 7 membered ring 3’,5’-bridged nucleoside analogs locked in a Southern conformation. These nucleoside analogues were converted in one pot to appropriate phosphoramidate prodrugs using boronate methodology. We also devised and prepared a novel carbocyclic nucleoside by replacing furanose with cyclohexene that resulted in a locked Northern conformation similar to LNA monomers. Further details on the biological activity and application for oligonucleotide synthesis will be discussed in detail.
Keywords:
locked nucleoside analogues; oligonucleotide synthesis
Available at various institutes of the ASCR
Novel conformationally locked nucleosides and nucleotides
We report on a synthesis of two novel types of conformationally locked nucleoside analogues. We prepared 7 membered ring 3’,5’-bridged nucleoside analogs locked in a Southern conformation. These ...
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