Abstract
In our work the influence of chemical modificatons and ions on RNA structure and dynamics has been tested. The effect of nucleotide modifications on E. coli and yeast tRNA in solution has been examined with a molecular dynamics approach. Simulations show a decrease of helical content in RNA secondary structure due to those modifications. In another step magnesium ion binding effects on the same tRNA were looked at by performing simulations with and without ions bound to tRNA. Ions coordinating nucleotides in those simulations show them highly affecting local secondary structure motifs. Thus the simulations performed give new hints on the function of nulceotide modifications and ion binding to RNA.
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