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Študija strukturnih motivov RNA zaporedij s ponovitvami adenina, gvanina in citozina
Levstek, Tevž (Avtor), Plavec, Janez (Mentor) Več o mentorju... Povezava se odpre v novem oknu

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Izvleček
Zaporedja DNA z določenimi motivi, ki vsebujejo ponovitve adenina, gvanina in citozina, se ob primernih pogojih zvijejo v AGCGA-kvadruplekse. Pri tem tvorijo GAGA in GCGC-kvartete, ki se med seboj naložijo v kvadrupleks, pri čemer je, za razliko od bolje poznanih G-kvadrupleksov, njihov nastanek neodvisen od prisotnih kationov ali pH. AGCGA-kvadrupleksa, ki bi ga tvorila RNA, do danes še niso odkrili. Ker bi obstoj RNA AGCGA-kvadrupleksov lahko pomenil posebne biološke vloge takih molekul ali predstavljal nove tarče za zdravila, smo se znotraj diplomske naloge lotili raziskovanja enega od RNA zaporedij s potencialno možnostjo tvorbe AGCGA-kvadrupleksov. Diplomsko delo je del širše raziskave, kjer smo preiskali večje število RNA zaporedij s ponovitvami adenina, gvanina in citozina, za katere je bilo dokazano, da njihova ekvivalentna DNA zaporedja tvorijo AGCGA-kvadruplekse. Raziskovano RNA zaporedje 5'-GCGA UU AGCG UU GCGA UU AGCG-3' je modelno zaporedje, ki bi potencialno lahko tvorilo paralelni monomolekularni AGCGA-kvadrupleks. Pri raziskovalnem delu smo uporabljali predvsem različne tehnike NMR spektroskopije, in sicer 1D protonski NMR, 1H-1H NOESY NMR in 1H-15N SOFAST- HMQC z uporabo ustrezno izotopsko označenih vzorcev, ter PAGE in CD-spektroskopijo. Dokazali smo, da zaporedje ne tvori AGCGA-kvadrupleksa v pogojih blizu fiziološkim (pH 7, koncentracija KCl 50 mM in koncentracija KPi 10 mM). Zaporedje namreč tvori vsaj tri različne strukture lasnice, ki so med seboj v ravnotežju. Predlagali smo tudi najverjetnejše strukture vseh treh lasnic. Predvidevamo, da se preučevano RNA zaporedje, podobno kot ostala zaporedja vključena v širšo študijo, ne zvije v AGCGA-kvadrupleks, najverjetneje zaradi dodatne 2'-OH skupine na sladkorju, ki preprečuje tvorbo stabilnih AGCGA-kvadrupleksov.

Jezik:Slovenski jezik
Ključne besede:RNA, AGCGA-kvadrupleks, sekundarna struktura, NMR
Vrsta gradiva:Diplomsko delo/naloga (mb11)
Tipologija:2.11 - Diplomsko delo
Organizacija:FKKT - Fakulteta za kemijo in kemijsko tehnologijo
Leto izida:2021
COBISS.SI-ID:78821123 Povezava se odpre v novem oknu
Število ogledov:43
Število prenosov:11
Metapodatki:XML RDF-CHPDL DC-XML DC-RDF
 
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Sekundarni jezik

Jezik:Angleški jezik
Naslov:Study of structural motifs of RNA sequences with adenine, guanine, and cytosine repeats
Izvleček:
DNA sequences with specific repeats of adenine, guanine, and cytosine fold into AGCGA-quadruplex under certain conditions. In doing so, they form GAGA and GCGC tetrads, which are stacked onto each other in a quadruplex, with the formation being independent of the cations present and the pH in contrast to the more well-known G-quadruplexes. AGCGA-quadruplex secondary structure formed by the RNA was never described. Since AGCGA-quadruplexes could represent new drug targets or have important biological roles, we have conducted research of one RNA sequence with potential ability to form above mentioned structure, as part of the thesis. Thesis is part of broader research in which we studied a larger number of RNA sequences with repeats of adenine, guanine and cytosine, for which DNA counterparts were proved to form AGCGA-quadruplexes. The investigated RNA sequence 5'-GCGA UU AGCG UU GCGA UU AGCG-3' is a model sequence that could potentially form a parallel monomolecular AGCGA-quadruplex. The study was performed by different NMR techniques, such as 1D proton NMR, 1H-1H NOESY NMR, 1H-15N SOFAST- HMQC with the usage of appropriately isotopically labelled samples and additionally PAGE and CD-spectroscopy. The sequence was shown not to form the AGCGA-quadruplex under conditions close to physiological (pH 7, KCl concentration 50 mM and KPi concentration 10 mM). The sequence was shown to form at least three different hairpin structures that are in equilibrium with each other. We also proposed the most probable structures of all mentioned hairpins. We presume that studied RNA sequence does not fold into AGCGA-quadruplex, similarly to other sequences included in broader study, most probably because of additional 2’-OH group on sugar, which prevents the formation of stable AGCGA-quadruplexes.

Ključne besede:RNA, AGCGA-quadruplex, secondary structure, NMR

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