A PROPOSAL FOR THE CONFORMATION OF LOOP-E IN ESCHERICHIA-COLI 5S RIBOSOMAL-RNA

A proposal is advanced for the conformation of the loop E region of pr okaryotic 5S rRNAs based on spectroscopic data obtained from pAD3 RNA, a construct that includes helix IV, helix V, and loops D and E from E scherichia coli 5S rRNA. Even though loop E juxtaposes bases that cann ot form Watson-Crick base pairs, it resembles an A-form double helix; its nucleotides relate to each other spectroscopically in a helix-like way and are in the anti conformation. The ends of loop E, which is pa lindromic, have the same conformation. Working in from either end towa rds the center of the loop, a closing GC is followed by a side-by-side GA and then by a reversed Hoogsteen AU, a pattern resembling that fou nd at one end of eukaryotic loop E. The center of the loop consists of three nucleotide pairs, which appear to be an asymmetric GG pair, a W atson-Crick-like AG, and a GU stabilized by a single hydrogen bond.