Abstract
Osmolytes such as urea and trimethylamine N-oxide (TMAO) accumulate in response to osmotic stress. Urea is known for its role as a protein destabilizer, while TMAO is known for its role as a protein stabilizer. However, the molecular mechanism by which these two osmolytes destabilize or stabilize RNA is not well understood. We perform multiple molecular dynamics (MD) simulations to determine the effects of urea and TMAO on RNA secondary structure using a RNA hairpin as a model system. From the simulations we are able to examine the molecular mechanism of the osmolytes' influence on the hairpin structure.
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