Elucidation of the Effects of the Cellular Environment on the UNCG Hairpin Motif

Abstract

The effects of osmolytes on nucleic acid chemistry are generally not as well understood as for their protein counterparts. Recent studies have shown that these effects are rather complex and show significant dependencies on the chemical and structural properties of both the nucleic acid and the cosolute. Osmolytes have the potential to affect the stability of secondary structure motifs and alter preferences for conserved stable nucleic acid sequences. The goal of this research is to contribute to the understanding of the in vivo function of nucleic acids by studying the effects of different classes of osmolytes on the UNCG tetraloop motif. UNCG tetraloops are the most common and stable of the RNA tetraloops and are nucleation sites for RNA folding. UNCG loops have also been found to have a thermodynamic preference for a CG closing base pair. The thermal denaturation of UNCG containing hairpins was monitored using UV-Vis spectroscopy in the presence and absence of a series of polyols and amine-based osmolytes. Generally, the osmolytes had little effect of the thermodynamic preference for a CG closing base pair, except for PEG 200, which significantly destabilized the loops with a CG closing base pair relative to those with a GC closing base pair. Moreover this significant difference appears to be specific to UNCG loops when compared to other related sequences, suggesting that PEG 200 may have preferential interactions with the UNCG sequences in the presence of a CG closing base pair.