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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 ...
Structure of an immunoactive polysaccharide isolated from Korean mulberry fruit (Morus alba L.)
Bleha, R.; Lee, J. S.; Capek, P.; Pohl, Radek; Kim, H. B.; Choi, D. J.; Lee, S.; Lee, J.; Jang, S. J.; Synytsya, A.; Park, Y. I.
2014 - English
A water-soluble polysaccharide (JS-MP-1) was isolated from the water extract of Korean white mulberry fruits (Morus alba L.) by ethanol precipitation and then purified by DEAE-cellulose ion exchange chromatography. Obtained final polysaccharide (1600 KDa) consisted of galactose, arabinose and rhamnose as major neutral sugars. JS-MP-1 also contains galacturonic and glucuronic acids (4:1). Sugar linkage, FTIR and correlation NMR analyses confirmed that it is a rhamnogalacturonan type I (RG I), which contains the alternating sequence of 1,4-alpha-D-GalAp and 1,2-alpha-L-Rhap units in the backbone. Neutral sugar side chains of JS-MP1 were identified as (1 -> 5)-alpha-L-arabinan and arabinogalactan type II (AG II) having the (1 -> 6)-beta-D-galactan core. The arabinan side chains are bound to the backbone at the O-4 position of some alpha-L-Rhap units, while the way of linkage between RG I and AG II chains is unclear. It was demonstrated that JS-MP-1 significantly stimulates murine macrophage RAW 264.7 cells to release chemokines (RANTES and MIP-1 alpha) and proinflammatory cytokines like INF-alpha and IL-6, and induce the iNOS and COX-2 gene expression, which are responsible for the production of NO and prostaglandin PGE2, respectively. These results suggest that JS-MP-1 can act as a potent immunomodulator and these observations may support the applicability of this polysaccharide or the water extracts of mulberry fruit can be used as an immunotherapeutic adjuvant or health beneficial food material.
Keywords:
pectic polysaccharides
Available at various institutes of the ASCR
Structure of an immunoactive polysaccharide isolated from Korean mulberry fruit (Morus alba L.)
A water-soluble polysaccharide (JS-MP-1) was isolated from the water extract of Korean white mulberry fruits (Morus alba L.) by ethanol precipitation and then purified by DEAE-cellulose ion exchange ...
Development and applications of ionization techniques in ambient mass spectrometry
Rejšek, Jan; Vrkoslav, Vladimír; Cvačka, Josef
2014 - English
Ambient mass spectrometry is a sharply developing subject area. Desorption electrospray ionization (DESI) and desorption atmospheric pressure photoionization (DAPPI) are two types of ionization techniques in the ambient mass spectometry. Herein, they were investigated in two research areas: (1) TLC analysis. (2) Localization of insect defense glands.
Keywords:
ambient mass spectrometry; desorption electrospray ionization; desorption atmospheric pressure photoionization; thin-layer chromatography; insect defense compounds; mass spectrometry imaging
Available at various institutes of the ASCR
Development and applications of ionization techniques in ambient mass spectrometry
Ambient mass spectrometry is a sharply developing subject area. Desorption electrospray ionization (DESI) and desorption atmospheric pressure photoionization (DAPPI) are two types of ionization ...
Analysis and characterization of antimicrobial peptides by capillary electromigration methods
Tůmová, Tereza; Monincová, Lenka; Čeřovský, Václav; Kašička, Václav
2014 - English
High-performance capillary electromigration methods (zone electrophoresis, affinity electrophoresis, isotachophoresis and micellar electrokinetic chromatography) have been applied to analysis and physicochemical characterization of halictines – antimicrobial peptides isolated from the bee Halictus sexcinctus.
Keywords:
antimicrobial peptides; capillary electrophoresis; coating
Available at various institutes of the ASCR
Analysis and characterization of antimicrobial peptides by capillary electromigration methods
High-performance capillary electromigration methods (zone electrophoresis, affinity electrophoresis, isotachophoresis and micellar electrokinetic chromatography) have been applied to analysis and ...
Analytical methods Used in the Studies on Chemical Ecology of Termites
Krasulová, Jana; Hanus, Robert; Sillam-Dusses, David; Žáček, Petr; Jiroš, Pavel; Šobotník, Jan; Kalinová, Blanka; Bosáková, Z.; Valterová, Irena
2012 - English
In this paper, I review our recent results on the trail-following communication in the Neotropical termite Glossotermes oculas (Serritermitidae) and the defensive chemistry of the African termite Psammotermes hybostoma (Rhinotermitidae). These findings belong to our current project focused on chemical ecology of critical termite genera from families Rhinotermitidae and Serritermitidae.
Keywords:
defensive compounds; GC-MS; GCxGC-MS; termites; trail-following pheromone
Available at various institutes of the ASCR
Analytical methods Used in the Studies on Chemical Ecology of Termites
In this paper, I review our recent results on the trail-following communication in the Neotropical termite Glossotermes oculas (Serritermitidae) and the defensive chemistry of the African termite ...
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