RNA recognition site of PP7 coat protein

The coat proteins of different single-strand RNA phages use a common protein tertiary structural framework to recognize different RNA hairpins and thus offer a natural model for understanding the molecular basis of RNA-binding speci®city. Here we describe the RNA structural requirements for bind-ing to the coat protein of bacteriophage PP7, an RNA phage of Pseudomonas. Its recognition speci®-city differs substantially from those of the coat proteins of its previously characterized relatives such as the coliphages MS2 and Qb. Using designed variants of the wild-type RNA, and selection of binding-competent sequences from random RNA sequence libraries (i.e. SELEX) we ®nd that tight binding to PP7 coat protein is favored by the exist-ence of an 8 bp hairpin with a bulged purine on its 5¢ side separated by 4 bp from a 6 nt loop having the sequence Pu-U-A-G/U-G-Pu. However, another structural class possessing only some of these features is capable of binding almost as tightly