Ribozymes fold in a completely different way to enzymes, witht the base pairs forming stem-loop structures. This is similar to tRNA structure, with the added complication that magnesium ions are needed to 'glue' the helices together.

The activity of a ribozyme is dependant primarily on its hydroxy groups, and any bound catalytic metal ions. The use of non-standard bases (as in tRNA) is possble, to allow the introduction of increased catalytic activity.