THEORETICAL AND EXPERIMENTAL SELECTION PARAMETERS FOR HBV-DIRECTED ANTISENSE RNA ARE RELATED TO INCREASED RNA-RNA ANNEALING

Annealing kinetics of antisense species against two different target r egions of the hepatitis B virus (HBV) were measured by kinetic in vitr o selection. Individual association rates were related to energies cal culated for local sequence segments and predicted structures of the co mplete pregenomic target RNA. A relationship between the presence of e xternal loops and joint sequences with fast pairing was observed where as internal loops did not favor fast RNA-RNA annealing. The findings w ere used to predict a fast-annealing HBV-directed antisense oligodeoxy ribonucleotide that turned out to pair with its target RNA at an assoc iation rate constant of k = 9.2 x 10(4) M-1 S-1, which is substantiall y faster than the annealing rates of artificial antisense RNA so far i ncluded in in vitro selection assays.