EFFECTS OF VARIATIONS IN LENGTH OF HAMMERHEAD RIBOZYME ANTISENSE ARMSUPON THE CLEAVAGE OF LONGER RNA SUBSTRATES

The efficacy of intracellular binding of hammerhead ribozyme to its cl eavage site in target RNA is a major requirement for its use as a ther apeutic agent, Such efficacy can be influenced by several factors, suc h as the length of the ribozyme antisense arms and mRNA secondary stru ctures. Analysis of various IL-2 hammerhead ribozymes having different antisense arms but directed to the same site predicts that the hammer head ribozyme target site is present within a double-stranded region t hat is flanked by single-stranded loops, Extension of the low cleaving hammerhead ribozyme antisense arms by nucleotides that base pair with the single-stranded regions facilitated the hammerhead ribozyme bindi ng to longer RNA substrates (e.g. mRNA). In addition, a correlation be tween the in vitro and intracellular results was also found, Thus, the present study would facilitate the design of hammerhead ribozymes dir ected against higher order structured sites. Further, it emphasises th e importance of detailed structural investigations of hammerhead riboz yme full-length target RNAs.