Role of Non canonical Base pairsand their higher order assemblies in RNA structure and function a Structural Bioinformatics Approach

Abstract

The work described in this thesis addresses different important aspects of RNA structural bioinformatics research, involving detailed structural and contextual analysis of RNA structural elements, which can facilitate the formulation of rules governing the remarkable structural and functional diversities of large RNA molecules. To understand the complex RNA structures and respective functions, a bottom-up approach is followed in my work, where characterization of the smaller and simpler structural elements have been carried out first to understand their putative functional roles in overall structural contexts. With the larger goal of strengthening the basis for future research within the RNA structure-function paradigm, the scope of this thesis may be defined, though not limited, by the following specific objectives: (i) meaningful annotation and classification of higher order RNA structural elements (assemblies of more than one nucleotide residues connected by base-pairing interactions), (ii) implementation of different algorithms for mining recurrent structural elements present in larger RNA molecules, (iii) systematic organization of available data related to occurrences, structures and stability of different RNA structural elements and development of databases which can interactively support complex queries for easy retrieval of customized information, and (iv) computational study to understand the stability of few important RNA structural elements using quantum mechanical (QM) methods. In addition, to demonstrate the importance of the work done for this thesis, a thorough background study has been carried out and reported. This provides a comprehensive review, highlighting the landmarks in the course of developments leading to its contemporary status, in the field of RNA structural bioinformatics newline