Four years ago, using in vitro selection, we developed the first example of a DNA enzyme. Since then, we have produced several additional examples, including a DNA enzyme that can be directed to cleave almost any targeted RNA under simulated cellular conditions. Compared with synthetic RNA enzymes, DNA enzymes are easier to prepare and are more stable in biological tissues. The enzyme binds the RNA substrate through Watson-Crick pairing, enabling us to target different RNAs simply by altering the sequence of the recognition domains. The catalytic efficiency of the enzyme is the highest of any known nucleic acid enzyme.
Catalytic efficiency is determined by the rate of enzyme-substrate association.
After binding, the substrate is cleaved by the enzyme, and the 2 cleavage products are released at an even faster rate, allowing the enzyme to turn over rapidly. Substrates that contain a single base mismatch relative to the enzyme are not cleaved efficiently because they are released from the enzyme faster than they are cleaved. The favorable kinetic properties of the 10-23 DNA enzyme make it an attractive candidate for development as a therapeutic agent. Chemical modifications have been introduced into the DNA enzyme to improve its stability and bioavailability. Because DNA enzymes were discovered so recently, little is known about their 3-dimensional structure.