A Geometrical Approach in Folding a Pseudoknot Motif within the E. Coli 16S-RNA

Abstract

Except for tRNA, the tertiary structure of RNA molecules are very little known. The many possibilities in the arrangement of different helices in space and the flexibility in the single- stranded loops that connect the helical regions make the modeling of the tertiary structure of RNA molecule a very complex task. Here, we introduce an approach to fold RNA tertiary structure based only on the information of the secondary structure and the stereochemistry of the molecule. This approach was used to construct an atomic structure of a pseudoknot (bases 500–545) in the E. coli 16S RNA. The resulting structure is a closely packed molecule that is consistent with the predicted secondary structure and stereochemically feasible. This new approach is very general and easily adaptable. Experimental data (e.g., NMR, fluorescence energy transfer, etc.), as they become available, can be incorporated directly into the approach to improve the accuracy of the modeled structure.