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Eucaryotic cells systems and their biotechnologycal applications
Porubiaková, Otília ; Obruča, Stanislav (oponent) ; Vorlíčková, Michaela (oponent) ; Brázda, Václav (vedoucí práce)
The submitted dissertation is divided into several parts. The first part deals with the interactions of the p53 protein and its isoforms with different potential DNA substrates under different experimental conditions. These are predominantly DNA and its non-canonical structural motifs, such as G-quadruplexes or cruciform structures, whose interactions have been studied in yeast isogenic systems or by in vitro methods. The seconds part deals with the bioinformatic analysis of the mentioned secondary DNA structures in different organismal groups, and the result is a set of publications that show their non-random distribution in the genome and their relationship with regulation. The last part of the work contains unpublished results, including the results of testing the effect of natural and synthetic substances on aging in model human cells.
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Eucaryotic cells systems and their biotechnologycal applications
Porubiaková, Otília ; Obruča, Stanislav (oponent) ; Vorlíčková, Michaela (oponent) ; Brázda, Václav (vedoucí práce)
The submitted dissertation is divided into several parts. The first part deals with the interactions of the p53 protein and its isoforms with different potential DNA substrates under different experimental conditions. These are predominantly DNA and its non-canonical structural motifs, such as G-quadruplexes or cruciform structures, whose interactions have been studied in yeast isogenic systems or by in vitro methods. The seconds part deals with the bioinformatic analysis of the mentioned secondary DNA structures in different organismal groups, and the result is a set of publications that show their non-random distribution in the genome and their relationship with regulation. The last part of the work contains unpublished results, including the results of testing the effect of natural and synthetic substances on aging in model human cells.
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DNA POLYMERASE STOP ASSAY FOR DETECTION OF G-QUADRUPLEXES
Petr, Marek ; Bažantová, Pavla ; Adámik, Matěj ; Kejnovská, Iva ; Dvořáková, Zuzana ; Vorlíčková, Michaela ; Pečinka, Petr ; Brázdová, Marie
In this work we performed DNA polymerase stop assays while using template DNA derived from promoter regions of VEGF and c-Myc proto-oncogenes under variety of experimental conditions. Partial stopping of DNA synthesis along the template strand was observed in the presence of K+ ions due to formation of stable G-quadruplex structures. In contrast, Na+ ions alone were unable to stabilize G-quadruplexes to stop the reaction at their site. These data suggest that K+ and Na+ ions, which are both known to stabilize G-quadruplexes, do this in different manner or extent.
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In situ study of nuclear acids interactions key for gene expression and therapy based on its silencing
Špringer, Tomáš ; Štěpánek, Josef (vedoucí práce) ; Brynda, Eduard (oponent) ; Vorlíčková, Michaela (oponent)
V dizertační práci studujeme nová analoga odvozená od R06 aptameru cílící na TAR vlásenku HIV viru s použitím citlivého biosensoru s povrchovými plasmony, který umožňuje sledování molekulárních interakcí v reálném čase. Vyšetřujeme sedm různých modifikací, které jsou umístěné na devíti pozicích R06 aptameru, a odhalujeme jejich použitelnost při tvorbě účinných a stálých anti-TAR oligonukleotidů. Dále zjišťujeme, které pozice jsou vhodné pro nahrazení modifikací, a zároveň interpretujeme výsledky v kontextu lokální nukleotidové geometrie a interakcí v TAR/anti-TAR komplexu. V dizertační práci dále vyvíjíme nový fluidický systém, který eliminuje disperzi vzorku a míšení vzorků, a tak umožňuje přesné sledování molekulárních interakcí na povrchu SPR čipu. Pro charakterizaci podmínek měření na povrchu oligonukleotidového čipu studujeme stínící efekt jednomocných a dvoumocných kationtů, které jsou klíčové pro interakci záporně nabitých oligonukleotidů.
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