Abstract
RNA folding plays an essential role for temperature dependent functions in cells. For example, RNA thermometers regulate translation of heat shock and virulence genes by folding and unfolding. Here, we employed the fourU RNA thermometer motif of Salmonella, a hairpin—structured RNA to study in-cell folding stability of an RNA hairpin and its in vitro stability which is perturbed by crowding and sticking agents. To discover the solvation environment that accounts for cellular crowding and sticking we conduct a two-dimensional scan of mixtures of artificial crowding and sticking agents, PEG10K (polyethylene glycol, 0-300 mg/ml) and M-PER buffer (Mammalian Protein Extraction Reagent, 0-80%).
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