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 se quence region. These RNAs interact with elongation factor Tu in both t he GTP and the GDP form. A slight preference for the GTP form of the p rotein 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 s ite 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', wh ich was also found in the alpha-sarcin domain of T. thermophilus 23S r RNA. The isolated RNAs have a hairpin structure with the 5'-ACCGAAG-3' sequence located in non-base-paired regions. Chemical probing and del etion experiments indicate that the consensus sequence is required for the interaction with elongation factor Tu.