Binding of U1A protein to the 3′ untranslated region of its pre-mRNA

Abstract

We have studied the global structure of the U1A 3′ untranslated region (UTR) element using fluorescence resonance energy transfer. Comparison of a single UTR-box with a series of oligoadenine bulges indicates that the UTR-box introduces a significant kink into the axis of the RNA, and quantification of the results suggests an included bend angle of approximately 100 ° (i.e. 80 ° from linear). The complete 3′-UTR element is also severely kinked by the two UTR-boxes. We can observe binding of U1A protein to the 3′-UTR element by a change in the fluorescence anisotropy of Cy3 attached to one of the helical ends. In parallel with the binding, we observe a marked increase in fluoresence resonance energy transfer efficiency between fluorophores attached at the two 5′ termini, indicating a significant change in global conformation induced by the binding of the protein.