Sequence Dependence of Stability for Group II Single Nucleotide Bulge Loops

Abstract

Thirty RNA duplexes containing group II single nucleotide bulge loops were optically melted in 1M NaCl, and the thermodynamic parameters DH°, DS°, DG°37, and TM for each sequence were determined. Group II bulge loops have two or more consecutive identical nucleotides at the bulge position such that there is ambiguity as to which nucleotide is the bulge. Sequences from this study were combined with sequences from a previous study (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 nearest‐neighbor model to predict the free energy of an RNA duplex containing a single nucleotide bulge. The free energy increments for the introduction of a group II bulge loop range from 0.9 and 7.3 kcal/mol. The introduction of the bulge was found in all cases to destabilize the duplex. As observed previously for Group I bulge loops (Blose et al., (2007) Biochemistry 46, 15123‐15135), neither the identity of the bulge nor its nearest neighbor had an effect on the destabilization of the duplex by the bulge. The influence of the bulge on the duplex stability was primarily affect by non‐nearest‐neighbor interactions. Specifically, there is a direct correlation between the destabilization of the duplex and the stability of the stems adjacent to the bulge.