RNA stem-loop microhelices with helix sequences based on tRNA acceptor stems can be charged with specific amino acids. Experiments were designed to test the possibility that microhelices could laterally associate through complementary loop sequences and thereby bring their attached aminoacyl groups close enough together to form a peptide bond. Computer simulations suggested that formation of such complexes would be sensitive to the number of loop nucleotides needed to span the grooves of the quasi-continuous helix of the intermolecular pseudoknot so formed. These predictions were conformed experimentally by observation of complex formation sensitivity to loop size. Complexes with optimized loop sizes had apparent bimolecular dissociation constants of approximately 100 nM with only three complementary base pairs between the respective loops. Single nucleotide substitutions that disrupted the predicted intermolecular loop-loop base-pairing abolished detectable association. Similarly, placing a gap between the short helix formed by loop-loop pairing and the adjacent acceptor stems also diminished complex formation. These experiments establish an experimental basis for microhelix association for peptide synthesis.