BEND AND HELICAL TWIST ASSOCIATED WITH A SYMMETRICAL INTERNAL LOOP FROM 5S RIBOSOMAL-RNA

We have used gel electrophoretic mobility measurements to investigate the conformation of the symmetric eubacterial loop E sequence of 5S rR NA (seven nucleotides in each strand). The loop strongly retarded the gel mobility of duplex RNAs containing it. In contrast, only asymmetri c A(5).A(n) or U-5.U-n internal loops (n not equal 5) strongly affecte d duplex RNA gel mobility. A phasing experiment, in which an A(2) bulg e and loop E were placed in the same duplex RNA and the number of base pairs between them varied, showed that loop E has a permanent bend an d is torsionally stiff. A second phasing experiment substituting loop E for duplex sequences between two A(2) bulges measured the helical tw ist associated with loop E; it is about 30 degrees (+/-15 degrees) ove rwound compared to a duplex RNA of the same number of bases. Ribosomal protein L25 specifically recognizes loop E but had little or no effec t on the twist of the loop. These results suggest that loop E adopts a specific, roughly helical structure.