A MODEL OF THE IRON-RESPONSIVE ELEMENT RNA HAIRPIN LOOP STRUCTURE DETERMINED FROM NMR AND THERMODYNAMIC DATA

The iron responsive element (IRE) is a conserved RNA structure that is found in the 5' UTR of ferritin mRNA and in the 3' UTR of transferrin receptor mRNA. It is the binding site of the iron responsive protein (IRP), and the interaction is part of the regulation of cellular iron metabolism The IRE six-nucleotide hairpin loop, 5'C(1)A(2)G(3)U(4)G(5) N(6), is conserved in sequence, and mutations have shown that it is re quired for IRP binding. On the basis of the thermodynamic and NMR expe riments utilized here, the IRE loop structure 5'C(1)A(2)G(3)U(4)G(5)C( 6), is described in detail. Measurements of loop stability show that i t has 2.9 kcal/mol more free energy than predicted. Nh4R data suggest that there is hydrogen bonding between C1 and G5 in a tertiary interac tion across the loop. A model structure, produced by MC-SYM/energy min imization, illustrates the conformational flexibility of U4 and C6, wh ich appear to exhibit considerable local motion in solution. NMR data indicate that the position of G3 is not well defined, leading to two f amilies of loop structures.