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Nucleic Acids Research, 1993, Vol. 21, No. 19 4627-4631
© 1993

RNA

The interaction between the iron-responsive element binding protein and its cognate RNA is highly dependent upon both RNA sequence and structure

Samie R. Jaffrey, David J. Haile, Richard D. Klausner and Joe B. Harford*

Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, National Institutes of Health Bethesda, MD 20892, USA

*To whom correspondence should be addressed at present address: RiboGene, Inc., 21375 Cabot Blvd., Hayward, CA 94545, USA

Received April 29, 1993. Revised August 13, 1993. Accepted August 13, 1993.

To assess the influence of RNA sequence2.urule;structure on the interaction RNAs 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 found in IRE stems significantly decreased the apparent affinity of the RNA for the IRE-BP. Similarly, alteration in the spacing and2.urule;or orientation of the loop and the unpaired cytosine of the stem by either increasing or decreasing the number of base pairs separating them significantly reduced efficacy as a competitor. It is inferred that the IRE-BP forms multiple contacts with its cognate RNA, and that these contacts, acting in concert, provide the basis for the high affinity of this interaction.


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