In vitro selected RNA molecules that bind to elongation factor Tu

RNA molecules which bind to elongation factor Tu from T. thermophilus were isolated from a pool of ribooligonucleotides with a randomized sequence region. These RNAs interact with elongation factor Tu in both the GTP and the GDP form. A slight preference for the GTP form of the protein was observed. The isolated RNA aptamers compete with each other for a common binding site on elongation factor Tu. This binding site is different from the binding site for aminoacyl-tRNA or the binding site for elongation factor Ts and is located on domain II of elongation factor Tu. The selected RNAs do not bind to elongation factor G. The EF-Tu binding RNAs share a short consensus sequence, 5'-ACCGAAG-3', which was also found in the alpha-sarcin domain of T. thermophilus 23S rRNA. The isolated RNAs have a hairpin structure with the 5'-ACCGAAG-3' sequence located in non-base-paired regions. Chemical probing and deletion experiments indicate that the consensus sequence is required for the interaction with elongation factor Tu.