The ribosomal S4-RNA fragment melts cooperatively when complexed with protein S4

Abstract

11). It binds to a large region at the 5’-end of 16 S RNA, defined as the S4-RNA [2-41, which can be prepared in large quantities by digestion of either renatured 16 S RNA or a protein S4-16 S RNA complex with carrier-bound pancreatic ribonuclease [4,5]. The S4-RNA binds exclusively protein S4 [2,4] and is the first cognate protein-binding site to be isolated from the 16 S RNA in large amounts. Previously, the topography of the RNA, in both the free S4-RNA and the protein-complexed form (S4-RNP), was compared by two approaches. (1) The location and 7% yield of each carrier-bound ribonuclease cut and sequence excision was approximately determined. It was found that whereas the positions of the cuts were the same in the S4-RNA and S4-RNP, the yields of the cuts were higher by a small but significant amount in the S4-RNP [3]. (2) The S4-RNA and S4-RNP were reacted with kethoxal such that accessible non-base paired guanines were modified [6]. Most of the modifi- cation sites were the same in the absence and presence of the protein, but the reactivity of a few sites increased significantly in the presence ofprotein S4. Both of these experiments suggested that some opening of the S4-RNA structure occurred as a result of protein binding. * Present