Thermodynamic characterization and nearest neighbor parameters for RNA duplexes under molecular crowding conditions

It is essential to study RNA under molecular crowding conditions to better predict secondary structures of RNAs in vivo. No systematic study has been completed to determine the effects of molecular crowding on RNA duplexes of varying lengths and sequence composition. Here, optical melting, circular dichroism, and osmometry data were collected for RNA duplexes in a 20% polyethylene glycol (with an average molecular weight of 200 g/mol) solution (PEG 200), and nearest neighbor parameters were derived using this data. RNA duplexes are destabilized, on average, 1.02 kcal/mol in the presence of 20% PEG 200. The ΔG°(37) values predicted by the nearest neighbor parameters for RNA duplexes in 20% PEG 200 were ∼0.65 kcal/mol closer to experimental ΔG°(37) values than those predicted by the standard nearest neighbor model. For one DNA sequence in solution with small crowders, the ΔG°(37) values predicted by the 20% PEG 200 RNA nearest neighbor parameters were closer to the experimental values than ΔG°(37) values predicted by either the RNA or DNA standard nearest neighbor models. This indicates that the nearest neighbor parameters for RNA duplexes in 20% PEG 200 may be generalizable to RNA and DNA duplexes in solutions with small crowding agents.