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• W2078707264 abstract "Fifty-nine RNA duplexes containing single-nucleotide bulge loops were optically melted in 1 M NaCl, and the thermodynamic parameters ΔH°, ΔS°, ΔG°37, and TM 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 °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 , , and are less destabilizing by 0.6 kcal/mol, and bulge sequences of the type and are more destabilizing by 0.4 kcal/mol than bulge loops adjacent to Watson−Crick base pairs." @default.
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• W2078707264 date "2007-11-30" @default.
• W2078707264 modified "2023-10-12" @default.
• W2078707264 title "Non-Nearest-Neighbor Dependence of the Stability for RNA Bulge Loops Based on the Complete Set of Group I Single-Nucleotide Bulge Loops" @default.
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• W2078707264 doi "https://doi.org/10.1021/bi700736f" @default.
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