Models for pairing of IS10 encoded antisense RNAs in vivo

Antisense regulation of IS10 transposase synthesis is mediated by a small RNA molecule, RNA-OUT which is complementary to the 5' region of the IS10 transposase mRNA, RNA-IN. Pairing between the two species in vivo prevents initiation of RNA-IN translation by steric occlusion of the ribosome binding site. The goal of this work is to develop a mathematical basis for antisense repression in vivo. Thus, by modeling antisense pairing as a biomolecular reaction in vivo, I have developed equations which relate the degree of translation inhibition to a relative pairing rate constant, k, and the in vivo RNA-OUT concentration. Using the methodology developed here, an analysis of mutations in the first three 5' bases of RNA-IN reveals a semi-logarithmic relationship between k and delta G, the estimated change in the free energy of pairing. Such correlations are not observed for mutations at other positions, implicating only the first three 5' bases of RNA-IN in the formation of a pairing nucleus with RNA-OUT. Finally, an analysis of mutations that affect antisense action at a post-nucleation step has been undertaken here and a specific model for how these mutations may affect antisense pairing is discussed.