RNA-RNA INTERACTIONS BETWEEN OLIGONUCLEOTIDE SUBSTRATES FOR AMINOACYLATION

RNA stem-loop microhelices with helix sequences based on tRNA acceptor stems can be charged with specific amino acids. Experiments were desi gned to test the possibility that microhelices could laterally associa te through complementary loop sequences and thereby bring their attach ed aminoacyl groups close enough together to form a peptide bond. Comp uter simulations suggested that formation of such complexes would be s ensitive to the number of loop nucleotides needed to span the grooves of the quasi-continuous helix of the intermolecular pseudoknot so form ed. These predictions were confirmed experimentally by observation of complex formation sensitivity to loop size. Complexes with optimized l oop sizes had apparent bimolecular dissociation constants of approxima tely 100 nM with only three complementary base pairs between the respe ctive loops. Single nucleotide substitutions that disrupted the predic ted intermolecular loop-loop base-pairing abolished detectable associa tion. Similarly, placing a gap between the short helix formed by loop- loop pairing and the adjacent acceptor stems also diminished complex f ormation. These experiments establish an experimental basis for microh elix association for peptide synthesis. (C) 1997 Elsevier Science Ltd.