Two- and Three-Dimensional Modeling of RNA Structure with NMR and Thermodynamics Methods.

摘要

RNA is a biopolymer that performs a variety of functions, such as storing genetic information, splicing, protein synthesis, chemical modification of other RNAs, and silencing gene expression. These functions were demonstrated to be affected by the structure of RNA. RNA folds in a hierarchical and sequential manner, first from sequence to secondary structure. This causes it to be suitable to prediction of secondary structure by computational algorithms. In this work, improvements to the accuracy of prediction of RNA secondary structure were achieved with an updated INN-HB model. NMR constraints that may assist with secondary structure prediction were identified. Separately, the 3D structure of an RNA hairpin from influenza A was determined.;Elucidation of secondary structure can facilitate accurate prediction of tertiary structure from local or long range interactions among elements of secondary structure. The INN-HB model provides a fast approach to folding secondary structure from sequence. The database of sequences from which the GU pair INN-HB model is derived was expanded and fitted to 11 parameters. An improvement in the accuracy of the model was demonstrated with statistical tests. For AU and GU pairs, two- and three-dimensional dependencies among chemical shifts of certain protons on the orientation of the base pairs in three base pair stacks were identified. These dependencies can be applied as constraints to a free energy minimization algorithm to improve the accuracy of secondary structure prediction. The 3D structure of a 39-nt construct of a hairpin with a 3? splice in a 2 x 2 internal loop from influenza A segment 7 mRNA was determined with NMR and restrained molecular dynamics. The hairpin loop consists of a GAAA stack enclosed by an unprotonated AC pair. The internal loop is structurally dynamic. The adenosine bulge forms a base triple with a canonical GC pair. The updated GU INN-HB model predicts a favorable DeltaG°37 for the secondary structure of this hairpin.