Jason A. Holland and Eric Cantu. Central Missouri State University, Warrensburg, MO
RNA triple helices are structural motifs consisting of a single stranded region of an RNA molecule binding in the major groove, through Hoogsteen interactions, to a Watson-Crick base paired hairpin. RNA triple helices can be intermolecular, formed from multiple RNA molecules, or intramolecular, formed from a single RNA. While research shows that intramolecular triple helices are inherently more stable than intermolecular, no study investigated intermolecular and intramolecular triple helices that consisted of the same sequence of base triples. This study investigates the stability difference between intermolecular and intramolecular triple helices consisting of the same base triple sequence. The effect that loop size and sequence has on the stability of intramolecular RNA triple helices is also investigated. Thermal denaturation and difference spectra were used to analyze the formation and stability of the RNA triple helices. Values for melting temperature and thermodynamic parameters delta H, delta S, and delta G will be presented.
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