Characterization of fragments of 16 S ribonucleic acid protected against pancreatic ribonuclease digestion by ribosomal protein S4.

Digestion of reconstituted complexes of 16 S RNA and ribosomal protein S4 with pancreatic ribonuclease, followed by resolution of the products on polyacrylamide gels of low ionic strength, gives rise to a protected ribonucleoprotein fragment with a mobility of 7 S. Fingerprinting of the RNA moiety indicates the presence of sequences covering the 5' one-third of the 16 S RNA. After its extraction from the acrylamide gels, the protected RNA from the complex can be separated into two components by sedimentation in sucrose gradients. One of these retains the ability to reassociate specifically with S4, as judged from its stoichiometry of binding in the presence of excess S4 and from its selection of S4 alone from a mixture of unfractionated 30S ribosomal proteins. It spans the same regions of the 16 S RNA as the total protected RNA, but lacks an internal sequence of about 120 nucleotides. This component contains a number of nicks which give rise to discrete bands upon electrophoresis in urea. The principal subfragments include Sections L through F (230 nucleotides), B through I'' (160 nucleotides), and part of section C'' (35 to 40 nucleotides). It is proposed that the binding site for S4 lies within these noncontiguous sequences, in support of the hypothesis that S4 makes multiple contacts with the 16 S RNA.