Characterizing Ribozyme Cleavage Reactions

Ribozymes are strands of RNA that are able to catalyze reactions. The ability to quantify accurately the catalytic activity of ribozymes is central to the process of defining their mechanisms of action. The catalyzed reaction is most commonly a trans -esterification reaction, resulting in cleavage of a strand of RNA that may or may not be part of the ribozyme strand. The aim of this chapter is to describe in detail the processes by which kinetic information can be extracted from a ribozyme-substrate system. The methods will be discussed with particular reference to hammerhead ribozymes, but some of the techniques may be applicable to other ribozymes.