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Development of a Bioinformatic System for Determination of the 3D Structure of RNA from Secondary Structure Constrains

Understanding cell life cycles, disease pathways and many other bio-organic phenomena in living organisms requires the study of RNA sequences and their secondary and tertiary structures. The various functions of this molecule (messenger, transfer, ribosomal, catalysts or enzymes) illustrate its importance, and the need for automatic tools enhancing its structural manipulation, the tertiary structure determination being a topic requiring still intense research efforts. Some seminal studies of this nature are those of Schlick [4], Shapiro et al. [1], Leclerc et al. [2], Zacharias and Sklenar [3]. The main characteristics of this works are the inclusion of multifunctional RNA structural information manipulation and exhaustive data base search tools [1], identification of common and distinguishing structural characteristics [2], conformational and energetic evaluation using a potential function [3]. Here we describe an approach to the prediction of the tertiary structure of RNA, from constrains posed by the evaluation of the secondary structure. The algorithm is based on a multidimensional search engine based on a simulated annealing method that predicts the conformation of bulges, stems and other secondary structure characteristics. Preliminary results output by the system indicate that, in spite of the huge conformational space to be searched conformers within a reasonable rmsd with those of reported crystal structures can be obtained. These can be later refined by energy minimization routines.