Design of Hybridizing Arms in Hammerhead Ribozymes

Hammerhead ribozymes as typically used in their trans -cleaving form are defined by their hybridizing arms, the remainder of the molecule being essentially constant. A major determinant of the nature of the hybridizing arms is their sequence, which is in turn determined by the sequence of the RNA at the cleavage site that is targeted. Therefore, the first step in designing hybridizing arms is to choose a target site. There are a number of methods that have been used. We will outline the techniques used without going into detail, because at least some of the techniques are the subject of other chapters in this book.