H-bonded base pairs containing a chemically modified nucleotide are recurrent structural motifs in RNA. Indeed, these functionally and structurally important recurrent pairs are often found to participate in tertiary interactions joining distant domains in functional RNA molecules. Our previous studies focused on the structure and stability of some of such conserved motifs in structurally important regions of tRNA molecules.1,2,3 Here in, we extend our survey and report on all possible instances of modified pairs present in the known experimental structures. We use high level quantum chemical methods, augmented with bioinformatics analysis on a dataset of high resolution crystal structures, to investigate the effect of the chemical modification on the interaction strength of the corresponding H-bonded base pair, as compared to its unmodified counterpart. We find that some of the modifications increase the stability of the base pair. Besides that, some of the modifications appear to be serving the structural role by aiding or blocking the H-bonding interactions with the surrounding nucleotides, thus affecting structural stability of the functional RNA molecules.                                                                             References:1. Oliva, R., Cavallo, L., Tramontano, A. Nucl. Acids Res.2006 , 34, 865.2. Oliva, R., Tramontano, A., and Cavallo, L. RNA 2007 , 13, 1427.3. Chawla, M., Sharma, P., Halder, S., Bhattacaryya, D. Mitra, A. J. Phys. Chem. B 2011 , 115, 1469.

Structural bioinformatics and quantum chemical studies of the effect of chemical modifications on the structure and stability of base pairs in functional RNAs

248th National Meeting (2014)

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