Analysis of the interaction between selected RNA-binding peptides and a target RNA containing a bulge and a GNRA-type tetraloop

: We have characterized the interaction between selected novel RNA-binding peptides and their target RNA. The RNA is comprised of two elements, a GCAA tetraloop, a member of the thermodynamically stable GNRA-type (where N is A or G, U, C; R is G or A) tetraloops, and a tri-purine bulge found in the frameshift stimutating structure on the human immunodeficiency virus type 1 (HIV-1) gag-pol mRNA. Peptides that bind specifically to the target RNA were selected from a combinatorial library based on arginine-rich motif (ARM) by a bacterial reporter system. We performed mutational studies using the reporter system and gel shift assays and found that the binding affinity and specificity of the RNA were mainly dependent on the GNRA-type tetraloop, and a modest contribution was also attributed to the bulge structure. Our finding reveals a novel mode of interaction by an RNA-peptide complex and expands our knowledge on the diversity of molecular recognition.