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MOLECULAR LEVEL UNDERSTANDING OF MODIFIED BASE PAIRS, NUCLEOBASE-LIGAND PSEUDO PAIRS AND ASSOCIATED HIGHER ORDER STRUCTURES IN FUNCTIONAL RNAAuthor: Preethi S P Date: 2018-04-12 Report no: IIIT/TH/2018/6 Advisor:Abhijit Mitra AbstractAlthough tremendous progress has been achieved towards understanding the biochemical versatility and biological functions of RNA, there is a need to deepen our understanding of the principles governing the structural and functional diversity of these fascinating biomacromolecules. One possible factor that contributes to the structural diversity of RNA is the presence of a variety of post-transcriptional modifications of the canonical nucleobases. Detailed analysis of the role of noncovalent interactions involving modified nucleobases in RNA is thus, expected to contribute to our understanding of the factors governing the structure and dynamics of RNA. In an attempt to contribute towards this theme, the present work employs a combination of sequence and structural bioinformatics techniques, along with quantum chemical calculations to understand the structure and strength of hydrogen bonded pairs and higher order structures involving post-transcriptionally modified nucleobases that are present in RNA macromolecular crystal structures. In addition to highlighting the important structural roles some of these hydrogen bonded entities in RNA molecules, our studies highlight the need for, and providing a comprehensive approach towards further investigations on such interactions in the context of many biological processes involving RNA. In addition to understanding the role of posttranscriptional modifications in RNA, we explored the structural and functional diversity exhibited by riboswitches, non-coding RNA, a class of RNA molecules that are a part of RNA regulatory networks, which specifically binds to small cognate ligands and regulate their turnover. Using QM and MD simulations, we explored the molecular features responsible for ligand recognition, and the associated role of noncovalent interactions in gene regulation by riboswitches. Overall, the thesis contributes towards understanding the structure-functional relationships in RNA macromolecules. Full thesis: pdf Centre for Computational Natural Sciences and Bioinformatics |
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