Quantum Chemical Studies of Structures and Stabilities of Natural and Synthetic Nucleic Acid Systems Electronic Structure Analysis of Noncovalent Interactions in Functional RNA and Modified DNA

Abstract

The present work deals with a detailed analysis of the structural and energetic newlinefeatures of base pairing interactions in RNA macromolecules. newlineCrystal structures of RNA molecules provide examples of a fascinating variety of newlinebase pairing interactions, which play an important role in maintaining their three newlinedimensional structures and in facilitating their functions. An accurate atomic newlinelevel description of interactions in these well defined structural building blocks newlineof RNA, and an understanding of their roles in higher order structures involving newlinerecurring motifs and tertiary interactions, is essential for understanding structurefunction relationship in these macromolecules. Some of these higher order structures and motifs are base triplets, quartets etc. in general, and dinucleotide newlineplatforms, kink-turn motifs etc. in particular. newlineIn the present work, a detailed analysis of base pairing geometries and interactions in RNA molecules is carried out using combined quantum chemical and newlinestructural (database) analysis methods. The role of base-base hydrogen bonding newlineinteractions in the formation of structural and functional motifs as mentioned newlineabove, is assessed. An effort has been made to project the conclusions drawn newlinefrom gas phase quantum chemical computations on RNA base pairs in a wide newlinebiochemical context of their occurence in macromolecular RNA structures. newlineIn addition, two theoretical investigations into specific structural and functional contexts in nucleic acid systems are carried out- one involving the analysis newlineof geometric and energetic features of ligand binding in a specific type of noncoding RNA- the purine riboswitches, and the other involving the interaction of newlinegold clusters with a novel type of synthetically modified DNA- the size expanded newlineDNA. newline