Aminoglycoside binding to human and bacterial A-site rRNA decoding region constructs

The 16S bacterial ribosomal A-site decoding rRNA region is thought to be th e pharmacological target for the aminoglycoside antibiotics. The clinical u tility of aminoglycosides could possibly depend on the preferential binding of these drugs to the prokaryotic A-site versus the corresponding A-site f rom eukaryotes. However, quantitative aminoglycoside binding experiments re ported here on prokaryotic and eukaryotic A-site RNA constructs show that t here is little in the way of differential binding affinities of aminoglycos ides for the two targets. The largest difference in affinity is 4-fold in t he case of neomycin, with the prokaryotic A-site construct exhibiting the h igher binding affinity. Mutational studies revealed that decoding region co nstructs retaining elements of non-Watson-Crick (WC) base pairing, specific ally bound aminoglycosides with affinities in the PM range. These studies a re consistent with the idea that aminoglycoside antibiotics can specificall y bind to RNA molecules as long as the latter have non-A form structural el ements allowing access of aminoglycosides to the narrow major groove. (C) 2 001 Published by Elsevier Science Ltd.