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 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 and/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.
Jaffrey
S R
SR
Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892.
Haile
D J
DJ
Klausner
R D
RD
Harford
J B
JB
D001483:Base Sequence; D001667:Binding, Competitive; D005293:Ferritins / Q000235:genetics*; D005786:Gene Expression Regulation; D006706:Homeostasis; D007501:Iron / Q000378:metabolism*; D035925:Iron-Regulatory Proteins; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D015345:Oligonucleotide Probes / Q000737:chemistry; D014176:Protein Biosynthesis; D012333:RNA, Messenger / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000378:metabolism*; D013329:Structure-Activity Relationship
D035925:Iron-Regulatory Proteins; D015345:Oligonucleotide Probes; D012333:RNA, Messenger; D016601:RNA-Binding Proteins; D005293:Ferritins; D007501:Iron