Poster abstracts

Poster number 49 submitted by Michael McCann

Non-nearest-neighbor dependence of the stability for RNA group II single nucleotide bulge loops

Michael D. McCann (Chemistry / Allegheny College), Geoffery F. S. Lim (Chemistry / Allegheny College), Michelle L. Manni (Chemistry / Allegheny College), Julie Estes (Chemistry / Allegheny College), Kelly A. Klapec (Chemistry / Allegheny College), Gregory D. Frattini (Chemistry / Allegheny College)

Abstract:
Thirty-one RNA duplexes containing single nucleotide bulge loops were optically melted in 1M NaCl; and, the thermodynamic parameters ÄH ^o, ÄS^o, ÄG^o₃₇, and T_m for each sequence were determined. The bulge loops were of the group II variety where the bulged nucleotide is identical to one of its nearest-neighbors leading to ambiguity as to the exact position of the bulge. Sequences from this study were combined with sequences from previous studies (Znosko et al., (2002) Biochemistry 41, 10406-10417), thus examining all possible group II single nucleotide bulge loop sequences. The combined data were used to develop a model to predict the free energy of an RNA duplex containing a single nucleotide bulge. As observed previously for group I bulge loops (Blose et al., (2007) Biochemistry 46, 15123-15135), neither the identity of the bulge nor the nearest-neighbor base pairs had an effect on the influence of the bulge loop on duplex stability. The destabilization of the duplex by the bulge was primarily related to the stability of the stems adjacent to the bulge. Specifically, there was a direct correlation between the destabilization of the duplex and the stability of the less stable duplex stem. Since there is an ambiguity of the bulge position for group II bulges, several different stem combinations are possible. The destabilization of group II bulge loops is similar to the destabilization of group I bulge loops, if the second least stable stem is used to predict the influence of the group II bulge. In-line structure probing of the group II bulge loop embedded in a hairpin indicates that the bulged nucleotide is the one positioned further from the hairpin loop.

References:
Blose JM, Manni ML, Klapec KA, Stranger-JonesY, Zyra AC, Sim V, Griffith CA, Long JD, Serra MJ. (2007). Non-nearest-neighbor dependence of the stability for RNA bulge loops based on the complete set of group I single-nucleotide bulge loops. Biochemistry 46, 15123-15135.

Znosko BM, Silvestri SB, Volkman H, Boswell B, Serra MJ. (2002). Thermodynamic parameters for an expanded nearest-neighbor model for the formation of RNA duplexes with single nucleotide bulges. Biochemistry 41, 10406-10417.

Keywords: group II bulge, duplex stability, in-line structure probing