THE INTERACTION BETWEEN THE IRON-RESPONSIVE ELEMENT-BINDING PROTEIN AND ITS COGNATE RNA IS HIGHLY DEPENDENT UPON BOTH RNA SEQUENCE AND STRUCTURE

To assess the influence of RNA sequence/structure on the interaction R NAs with the iron-responsive element binding protein (IRE-BP), twenty eight altered RNAs were tested as competitors for an RNA corresponding to the ferritin H chain IRE. All changes in the loop of the predicted IRE hairpin and in the unpaired cytosine residue characteristically f ound in IRE stems significantly decreased the apparent affinity of the RNA for the IRE-BP. Similarly, alteration in the spacing and/or orien tation of the loop and the unpaired cytosine of the stem by either inc reasing or decreasing the number of base pairs separating them signifi cantly reduced efficacy as a competitor. It is inferred that the IRE-B P forms multiple contacts with its cognate RNA, and that these contact s, acting in concert, provide the basis for the high affinity of this interaction.