IIIT Hyderabad Publications |
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Identification and Classification of Base-Base Stacking Interactions in Functional RNA MoleculesAuthor: Ayush Jhunjhunwala Date: 2019-12-13 Report no: IIIT/TH/2019/128 Advisor:Abhijit Mitra AbstractThe structure and dynamics of RNA macromolecules is influenced by myriad of noncovalent inter-actions, among which base pairing and base stacking are the most prominent. Detailed understanding of such interactions in the rapidly growing number of 3D RNA structures necessitates their proper an-notation and classification. Despite previous significant efforts toward classification of base pairing interactions in RNA, analogous scheme for classification of base stacking interactions is currently missing in literature. As a first step towards understanding the role of base stacking in various functional contexts of RNA, the present work provides an unambiguous and detailed classification scheme for RNA base stacks, in which the stacks are classified in terms of the mutual orientation of the interacting nucleobase faces, the mutual glycosidic orientation of the stacked nucleotides and the identity of the interacting rings. Further, an algorithm was developed for automated identification and classification of base stacks occurring in RNA crystal structures, which enabled us to identify exemplars of each stacking type, as well as carry out statistical distribution of different types of stacking contacts. The algorithm was further modified to analyse stacking interactions involving unique post-transcriptionally modified nucleobases. Finally, the utility of out classification scheme as well as automated stacking detection method was demonstrated by analysing the stacking interactions involved in specific structural and functional contexts of RNA. Overall, this study is expected to deepen our understanding of how different physicochemical forces contribute towards shaping the RNA structure-function landscape. Full thesis: pdf Centre for Computational Natural Sciences and Bioinformatics |
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