Interactions between 23S rRNA and tRNA in the ribosomal E site

Interactions between tRNA or its analogs and 233 rRNA in the large ribosoma l subunit were analyzed by RNA footprinting and by modification-interferenc e selection. In the E site, tRNA protected bases G2112, A2392, and C2394 of 23S rRNA. Truncated tRNA, lacking the anticodon stem-loop, protected A2392 and C2394, but not G2112, and tRNA derivatives with a shortened 3' end pro tected only G2112, but not A2392 or C2394. Modification interference reveal ed C2394 as the only accessible nucleotide in 23S rRNA whose modification i nterferes with binding of tRNA in the large ribosomal subunit E site. The r esults suggest a direct contact between A76 of tRNA A76 and C2394 of 233 rR NA. Protections at G2112 may reflect interaction of this 233 rRNA region wi th the tRNA central fold.