![]() Over 80% of the human genome is transcribed into RNA, but <3% of the RNA codes for proteins ( 1, 2). This confirms the need for the additional sequence dependence in the model. ![]() The average absolute difference between measured and predicted free energy changes at 37☌ for these three duplexes containing terminal adjacent AU and GU pairs improved from 1.38 to 0.27 kcal/mol. Introduction of the additional terms was tested with three optical melting experiments. The improved understanding of helix end stability, however, makes the separate treatment unnecessary. Prior parameter sets treated 5′GGUC3′ paired to 3′CUGG5′ separately from other 5′GU3′/3′UG5′ stacks. This refined understanding of helix ends facilitates fitting terms for base pair stacks with GU pairs. New nearest neighbor parameters that include this additional sequence dependence accurately predict the measured values of 271 helices in an updated database with a correlation coefficient of 0.982. Analysis of the updated database shows that terminal penalties depend on the sequence identity of the adjacent penultimate base pair. ![]() We curated an expanded database of helix stabilities determined by optical melting experiments. ![]() For helices, current parameters penalize terminal AU base pairs relative to terminal GC base pairs. Nearest neighbor parameters for estimating the folding stability of RNA secondary structures are in widespread use. ![]()
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