AN ANTIBIOTIC-BINDING MOTIF OF AN RNA FRAGMENT DERIVED FROM THE A-SITE-RELATED REGION OF ESCHERICHIA-COLI 16S RIBOSOMAL-RNA

A small RNA derived from the decoding region of Escherichia coli 16S r RNA can bind to antibiotics of aminoglycosides (neomycin and paromomyc in) that act on the small ribosomal subunit [Purohit,P. and Stern,S. ( 1994) Nature, 370, 659-662]. In the present study, the P-site subdomai n was removed from this decoding region RNA to construct a 27mer RNA ( designated as ASR-27), which includes the A-site-related region (posit ions 1402-1412 and 1488-1497) of 16S rRNA, Footprint experiments with dimethyl sulfate as a chemical probe indicated that the ASR-27 RNA can interact with the neomycin family in the same manner as the decoding region RNA, A mutagenesis analysis of the ASR-27 RNA revealed that par omomycin binding of ASR-27 involves the C1407 . G1494 and C1409 . G149 1 base pairs, and the internal loop comprising A1408 and the nucleotid es in positions 1492-1493, located between the two C . G base pairs, I n addition, a G or U in position 1495, and base pairing between positi ons 1405 and 1496 are also involved, These structural features were fo und in a viral RNA element, the Rev-binding site of human immunodefici ency virus type-1, which may explain why neomycin can bind to this vir al RNA.