IIIT Hyderabad Publications |
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On the diverse roles of Nucleobases in shaping RNA structures and Functions - a QM based insightAuthor: Antarip Halder Date: 2018-06-27 Report no: IIIT/TH/2018/26 Advisor:Abhijit Mitra AbstractConsequent to the discovery of their catalytic and regulatory functions, RNA has been found to be associated with numerous biological processes including regulation of gene expression and protein synthesis. To participate in these cellular processes, RNA molecules are required to be folded into functionally competent structures. Unlike double stranded DNA, the single stranded RNA folds onto itself and thereby displays a diverse repertoire of noncanonical base pairs. Unique geometry, stability and physicochemical properties of these base pairs define the structural landscape of RNA molecules. In this regard, modification of nucleobases constitute an important feature. On one hand, they in- crease the diversity in RNA’s structural alphabets and, on the other, the subsequent changes in their respective electronic properties give rise to a new class of noncanonical base pairs. Interestingly, some nucleobase modifications remain ‘invisible’ even in the high resolution X-ray crystal structures (e.g., protonations, tautomerization, etc.), and can only be inferred through circumstantial evidences. In this thesis quantum mechanics (QM) based methods in conjunction with structural bioinformatics tech- niques have been implemented to study the putative roles of four different nucleobase modifications (e.g. metal ion binding, protonation, tautomerization and synthetic modification) in determining the geometry, stability and function of different noncanonical base pairs observed in functional RNAs. It has been illustrated here that Mg2+ binding not only can stabilize the intrinsically unstable ge- ometry of numerous important RNA base pairs, but also may fine tune their geometries and interaction energies. Among these base pairs, some are also stabilized by Class II nucleobase protonation (i.e., when the loaded proton is not sequestered between two bases). By evaluating the optimized geometries and interaction energies of such base pairs, in the presence and absence of protonation, a proof of con- cept has been established for a strategy to detect hitherto undetected occurrence of N7 and N3 proto- nated guanine base pairs. This also opens up the possibility of the discovery of undetected protonation in other base pairing systems. Consequences of nucleobase protonation has also been studied for base triples, which reveal that nucleobase protonation often leads to cooperative binding of three distantly placed nucleotides. In the context of protein synthesis, it is known that selection of wrong aminoacyl tRNA due to mismatch primarily at the first two positions of the codon-anticodon (C-AC) helix leads to missense errors. Recent crystal structures of complete 70S ribosome revealed that GU mismatches may occur at the first position of C-AC helix, where they mimic the GC like canonical geometry. It has been argued here that nucleobase tautomerization (enolic forms of uracil/guanine) is necessary for such spatial mimicry and is sufficient to maintain the overall interaction of the first C-AC pair with the monitoring residue (A1493) of 16S rRNA. In addition to the aforementioned findings, modified nu- cleobases have been studied, in the light of their important application in biomimetics and RNA based nanotechnology. In this work it has been evaluated why substitution of thymine by 6-Ethynylpyridone (a synthetic thymine analogue) increases the thermostability of double helical stretches. Overall, this thesis highlights that geometry and stability of RNA base pairs are sensitive towards different types of nucleobase modifications. Characterization of such sensitivity enriches the understanding about the sequence-structure-function relationship in RNA. Full thesis: pdf Centre for Computational Natural Sciences and Bioinformatics |
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