Introduction

Considering the variety of known RNA enzymes and the similarity of DNA and RNA, it seems reasonable that DNA can function as an enzyme as well. Through the use of in vitro selection techniques, we obtained a DNA enzyme that catalyzes the Pb²⁺-dependent cleavage of an RNA phosphoester in a reaction that proceeds with rapid turnover.

Result

Beginning with a population of 10¹⁴ random 50mer DNAs, we carried out five successive rounds of selective amplification, enriching for individuals that best promote the cleavage of a target ribonucleoside 3 '-O-P bond embedded within an otherwise all-DNA sequence. By the fifth round, the population as a whole carried out this reaction at a rate of 0.2 min^-1. Based on the sequence of 20 individuals isolated from this population, we designed a simplified version of the catalytic domain that operates in an intermolecular context with a turnover rate of 1 min^-1. This rate is more than 10⁵-fold increased compared to the uncatalyzed reaction.

Conclusions

The synthetic DNA enzyme obtained in this study functions with a rate that compares favorably to that of known RNA enzymes. Considering that we were able to produce this molecule from random sequences in only four days, we expect that many other examples of DNA enzymes will soon be forthcoming.