Natural RNAs often contain terminal loops consisting of GNRA (N=A, G, C, U;
R=A, G) and their receptors, which bind to the loops via long-range RNA-RN
A interactions. Among several known receptors, two characteristic structura
l elements have been identified that are termed the 11-nt motif (CCUAAG-UAU
GG) and IC3 motif (CCCUAAC-GAGGG). These two motifs that share a similar se
condary structure have been shown to exhibit distinctively different bindin
g specificities. The 11-nt motif recognizes a GAAA loop with highest specif
icity among the known receptors, whereas the IC3 motif distinguishes GAAA f
rom other GNRA loops less stringently than any other receptors. To identify
the elements in the receptors that determine the binding specificity, a se
ries of chimeric receptors derived from the two motifs were prepared and th
eir properties were examined. We identified characteristic base-pairs and a
particular U residue in the receptors as such elements by means of a gel m
obility shift assay that evaluates the degree of the tetraloop-receptor int
eraction. The relationship between the elements and the specificity is disc
ussed together with a model that describes a possible evolutional linkage b
etween the two receptors.