The ribosomal A-site as an inspiration for the design of RNA binders.
The specific binding of aminoglycoside antibiotics to the bacterial ribosomal decoding site (A-site) has inspired the study of RNA-small molecules interactions and the search for novel RNA binders. Among the numerous RNA targets studied so far, the A-site holds a unique place. It is among the few truly validated RNA targets for which naturally occurring ligands have been discovered as "cognate" binders. In addition, due to its encapsulating architecture, the A-site is a more discriminating RNA target when compared to other RNA sequences. Previous observations and current challenges for the designers of potent and specific RNA binders are discussed.
Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0358, USA. ytor@ucsd.edu
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D000900:Anti-Bacterial Agents / Q000737:chemistry / Q000494:pharmacology; D001665:Binding Sites / Q000235:genetics; D015394:Molecular Structure; D009355:Neomycin / Q000737:chemistry / Q000494:pharmacology; D009690:Nucleic Acid Conformation / Q000187:drug effects; D010303:Paromomycin / Q000737:chemistry / Q000494:pharmacology; D012336:RNA, Ribosomal, 16S / Q000737:chemistry* / Q000235:genetics; D012270:Ribosomes / Q000235:genetics / Q000378:metabolism*; D013329:Structure-Activity Relationship
D000900:Anti-Bacterial Agents; D012336:RNA, Ribosomal, 16S; D010303:Paromomycin; D009355:Neomycin