CORONATION: Comparison of RibO Nucleic Acid Tertiary’s Involving Overlapping Network

Abstract

A fast approach to compare RNA tertiary structures has been developed. This study considers RNA structures as collection of points (atoms) in three dimensional coordinates. This comparison is completely independent of nucleotide (base) order in sequence of RNA molecules. The CORONATION matches single nucleotides between two different RNA structures by looking at their three dimensional coordinates regardless of their relative sequential position. This method works by using description of geometrical patterns within each RNA structure based on graph theory. It finds similar 3D arrangements of bases among different structures by identifying overlapping between two structures. This overlap can be either a particular motif of RNA or a general matching of RNA chain (surface). This paper presents extended results of our previous work and further extension in generalization and exactness of the algorithm. This efficient technique compares two RNA molecules in short possible time (mostly in a fraction of a minute). We have compared RNA structures with each other and successfully detected a good number of structures that show their overlapping score. We have particularly compared tRNA structures against the other families of RNA structure present in Protein Data Bank (PDB). Besides detecting similar patterns for tRNA, we spotted the motifs in different RNA families such as Saccharomyces cerevisiae (S.C) and Escherichia coli (E.Coli), etc. These motifs are well known and have been inspected by different procedures before. This study has many advantages and implications for diseases detection, RNA folding, evolution, and can be used to search for pharmacophoric patterns