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

We have studied the global structure of the U1A 3' untranslated region (UTR ) element using fluorescence resonance energy transfer. Comparison of a sin gle 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 degree s (i.e. 80 degrees from Linear). The complete 3'-UTR element is also severe ly kinked by the two UTR-boxes. We can observe binding of U1A protein to th e 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 mar ked increase in fluoresence resonance energy transfer efficiency between fl uorophores attached at the two 5' termini, indicating a significant change in global conformation induced by the binding of the protein. (C) 1999 Acad emic Press.