pH dependent conformational changes within the iron responsive element

The expression of several mRNAs related to iron importation, storage and utilization within mammalian cells are regulated through interactions of iron regulatory proteins with an iron responsive element, an RNA hairpin with a bulged C. A dimethylsulfate modification interference assay was used to demonstrate that the iron responsive element undergoes significant pH dependent conformational changes. Specifically, it was demonstrated that the phylogenetically conserved A within the hairpin loop and an intra-loop C-G base pair are highly sensitive to changes in pH. The conserved C of the bulged loop does not significantly affect the pH dependent conformational changes of the hairpin loop. These studies have structural implications for an RNA-protein interaction that is critical to mammalian iron regulation.