MODELS FOR PAIRING OF IS10 ENCODED ANTISENSE RNAS IN-VIVO

Antisense regulation of IS10 transposase synthesis is mediated by a sm all RNA molecule, RNA-OUT which is complementary to the 5' region of t he IS10 transposase mRNA, RNA-IN. Pairing between the two species in v ivo prevents initiation of RNA-IN translation by steric occlusion of t he ribosome binding site. The goal of this work is to develop a mathem atical basis for antisense repression in vivo. Thus, by modeling antis ense pairing as a bimolecular reaction in vivo, I have developed equat ions which relate the degree of translation inhibition to a relative p airing 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 betwe en k and Delta G, the estimated change in the free energy of pairing. Such correlations are not observed for mutations at other positions, i mplicating only the first three 5' bases of RNA-IN in the formation of a pairing nucleus with RNA-OUT. Finally, an analysis of mutations tha t affect antisense action at a post-nucleation step has been undertake n here and a specific model for how these mutations may affect antisen se pairing is discussed.