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.
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