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MD simulation studies to investigate iso-energetic conformational behaviour of modified nucleosides m2G and m2 2G present in tRNA

Rohit Bavi,Susmit B. Sambhare,K. Sonawane

Published 2013 in Computational and Structural Biotechnology Journal

ABSTRACT

Modified nucleic acid bases are most commonly found in tRNA. These may contain modifications from simple methylation to addition of bulky groups. Methylation of the four canonical nucleotide bases at a wide variety of positions is particularly prominent among the known modification. Methylation of N2 group of guanine is a relatively common modification in tRNA and rRNA. N2-methylguanosine (m2G) is the second most often encountered nucleoside in E. coli tRNAs. N2, N2- dimethylguanosine (m2 2G) is found in the majority of eukaryotic tRNAs and involved in forming base pair interactions with adjacent bases. Hence, in order to understand the structural significance of these methylated nucleic acid bases we have carried out molecular dynamics simulation to see the salvation effect. The results obtained shows iso-energetic conformational behaviors for m2G and m2 2G. The simulation trajectory of m2G shows regular periodical fluctuations suggesting that m2G is equally stable as either s-cis or s-trans rotamers. The two rotamers of m2G may interact canonically or non-canonically with opposite base as s-trans m2G26:C/A/U44 and s-cis m2G26:A/U44. The free rotations around the C-N bond could be the possible reason for these iso-energetic conformations. Dimethylation of G has almost no influence on base pairing with either A or U. Thus, these results reveal that modified nucleosides m2G and m2 2G may play an important role to prevent tRNA from adopting the unusual mitochondrial like conformation.

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