Protein-Binding Sites on RNA

To determine the binding sites of proteins on the rRNA different methods have been used, most notably enzymatic digestion of the rRNA around the protein that protects the RNA binding site from nuclease attack. Details and results of these studies have been reviewed (Zimmer-mann, 1980 Wittmann, 1982 Brimacombe et al., 1978, 1983). The binding sites so obtained vary in length from about 50 nucleotides for protein S8 to about 500 nucleotides for protein S4. The 5 region of the 16 S rRNA contains the sites for proteins S4, S12, and S20. The 3  

Similar experiments on the 23 S rRNA molecule have shown binding regions for the 50 S proteins extending from about 50 nucleotides for LI 1 to about 500 nucleotides for L24 (Fig. 14). Proteins L3 and L16 bind to the 3 end of the 23 S rRNA, whereas the 5 end interacts with proteins L4, LI 1, and the (L7/L12)4 LIO complex. The central portion of the rRNA interacts with proteins L2 and L13 (Zimmermann, 1980 Brimacombe et al., 1983). 

Studies were done in order to precisely define the interactions taking place between specific nucleoddes on the RNA and amino acids on the proteins (Maly et al., 1980). Although these analyses are extremely difficult, several such interactions have been recently characterized in this way (Wower et al., 1981). 

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