Bend and helical twist associated with a symmetric 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 rRNA (seven nucleotides in each strand). The loop strongly retarded the gel mobility of duplex RNAs containing it. In contrast, only asymmetric A5.An or U5.Un internal loops (n not equal to 5) strongly affected duplex RNA gel mobility. A phasing experiment, in which an A2 bulge 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 and is torsionally stiff. A second phasing experiment substituting loop E for duplex sequences between two A2 bulges measured the helical twist associated with loop E; it is about 30 degrees (+/- 15 degrees) overwound compared to a duplex RNA of the same number of bases. Ribosomal protein L25 specifically recognizes loop E but had little or no effect on the twist of the loop. These results suggest that loop E adopts a specific, roughly helical structure.