Aminoacyl-tRNA conformation. Information from steroid and oligonucleotide probes

The conformations of aminoacyl- and deacylated tRNA Phe (yeast) have been compared by using the steroid progesterone and the tetranucleotides U-C-C-C and C-G-A-A as probes of transfer RNA ordered structure. U-C-C-C is complementary to G18-G19-G20-A21 in the dihydrouridine loop and C-G-A-A is complementary to T54-psi55-C56-G57 in the ribosylthymine loop. None of the probes bound to deacylated tRNA Phe but all three bound to phenylalanyl-tRNA Phe, with molar association constants of the order of 10(4) M-1. The oligonucleotide binding data imply that the tertiary hydrogen bonds between G18 and psi55, G19 and C56, T54 and m1A58, and A21 and the ribose of U8 (Quigley, G. J., Wang, A. H. J., Seeman, N. C., Suddath, F. L., Rich, A., Sussman, J. L., and Kim, S. H., (1975) Proc. Natl. Acad. Sci. U.S.A. 72, 4866-4870) are destabilized or broken on aminoacylation, unmasking the sequence T-psi-C-G thought to be involved in ribosome binding of aminoacyl-tRNA. The presumed progesterone binding site is G18-G19-G20, which is part of the binding site for U-C-C-C. Competition was not, however, observed between these two probes; model building has shown that they could, theoretically, bind simultaneously. Since progesterone bound to N-acetyl-Phe-tRNA Phe, the introduction of the additional positive charge on aminoacylation is not sufficient per se to explain the conformational change. The association of progesterone with peptidyl-tRNA Phe was similar to that with aminoacyl-tRNA Phe, implying that no further conformational change takes place in the region of the steroid binding site on formation of a peptide bond.