Poster abstracts

Poster number 48 submitted by Jessica Morelli

A Thermodynamic Study of Multiple Bulge Loops in RNA Duplexes

Laura E. Jones (Department of Chemistry, Allegheny College), Jessica N. Morelli (Department of Chemistry, Allegheny College), Martin J. Serra (Department of Chemistry, Allegheny College)

Abstract:
RNA oligomers containing two single bulge loops were analyzed to determine the thermodynamic parameters (ΔH ^o, ΔS ^o, ΔG ₃₇ ^oand T _M) through optical melting in 1 M NaCl. The second bulge loop was evaluated in 16 duplexes where the bulge was positioned on the same side of the duplex as well as on the complimentary strand. The duplex between the bulge loops, the inner duplex, was varied in length and sequence in addition to the orientation of the bulge. Inner duplexes consisting of two to four A-U and G-C base were evaluated with both bulges placed on the same side. Duplexes with the bulges on opposite strands that were composed of two to six G-C or A-U base pairs or a combination of G-C and A-U pairings were also examined. The thermodynamic data was compared to the current bulge loop prediction model (Blose, Silverman, and Bevilacqua, Biochemistry 2007, 4232-4240). The Blose model is not accurate in determining the destabilizing effect of two single base bulges because the second bulge affects the duplex differently from the first bulge. However, the Blose model does accurately predict that the bulge becomes less destabilizing as the adjacent stem becomes less stable. A larger data set should be examined in order to determine the effect of a second single base bulge loop in a duplex.

References:
Blose J.M., Silverman S.K., Bevilacqua P.C. (2007) A Simple Molecular Model for Thermophilic Adaption of Functional Nucleic Acids. Biochemistry 2007, 4232-4240.

Keywords: RNA thermodynamics, bulge loops