A comparative study on two GNRA-tetraloop receptors: 11-nt and IC3 motifs

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.