Non-Nearest-Neighbor Dependence of the Stability for RNA Bulge Loops Based on the Complete Set of Group I Single-Nucleotide Bulge Loops

• Published in: Biochemistry (Easton) 2007-12, Vol.46 (51), p.15123-15135
• Main Authors: Blose, Joshua M, Manni, Michelle L, Klapec, Kelly A, Stranger-Jones, Yukiko, Zyra, Allison C, Sim, Vasiliy, Griffith, Chad A, Long, Jason D, Serra, Martin J
• Format: Article
• Language: English
• ISSN: 0006-2960
• DOI: 10.1021/bi700736fPII:S0006-2960(70)00736-5

Fifty-nine RNA duplexes containing single-nucleotide bulge loops were optically melted in 1 M NaCl, and the thermodynamic parameters DeltaH degree , DeltaS degree , DeltaG degree sub(37), and T sub(M) for each sequence were determined. Sequences from this study were combined with sequences from previous studies [Longfellow, C. E., et al. (1990) Biochemistry 29, 278- 285; Znosko, B. M., et al. (2002) Biochemistry 41, 10406-10417], thus examining all possible group I single-nucleotide bulge loop and nearest- neighbor sequence combinations. The free energy increments at 37 degree C for the introduction of a group I single-nucleotide bulge loop range between 1.3 and 5.2 kcal/mol. The combined data were used to develop a model for predicting the free energy of a RNA duplex containing a single-nucleotide bulge. For bulge loops with adjacent Watson-Crick base pairs, 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 proposed model for prediction of the stability of a duplex containing a bulged nucleotide was primarily affected by non-nearest-neighbor interactions. The destabilization of the duplex by the bulge was 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. The stability of a duplex containing a bulged nucleotide adjacent to a wobble base pair also was primarily affected by non-nearest-neighbor interactions. Again, there was a direct correlation between the destabilization of the duplex and the stability of the less stable duplex stem. However, when one or both of the bulge nearest neighbors was a wobble base pair, the free energy increment for insertion of a bulge loop is dependent upon the position and orientation of the wobble base pair relative the bulged nucleotide. Bulge sequences of the type [eqn], [eqn], and [eqn] are less destabilizing by 0.6 kcal/mol, and bulge sequences of the type [eqn] and [eqn] are more destabilizing by 0.4 kcal/mol than bulge loops adjacent to Watson-Crick base pairs.