DNAzyme

DNAzyme, short for deoxyribozyme, is a DNA molecule that functions as a catalyst. Like ribozymes, DNAzymes accelerate chemical reactions, most commonly the site-specific cleavage of RNA substrates. They are identified by in vitro selection from random DNA libraries and rely on folding into active three-dimensional structures. Unlike protein enzymes, DNAzymes are nucleic acids and can be chemically synthesized with relative ease and stability.

RNA-cleaving DNAzymes are the most developed class. The best known examples are the 8-17 and 10-23 DNAzymes, which catalyze phosphodiester bond cleavage in RNA in a metal-ion-dependent manner. Each consists of a catalytic core surrounded by short binding arms that hybridize to the target RNA, directing cleavage at a specific site. The reaction typically produces a 2',3'-cyclic phosphate and a 5'-hydroxyl terminus.

Applications include gene regulation studies, where DNAzymes can knock down target transcripts in vitro and in cells; and diagnostic and biosensing technologies, where DNAzymes serve as programmable components in sensors for nucleic acids, metal ions, and other analytes. DNAzymes can be engineered with chemical modifications to increase nuclease resistance and binding affinity, enhancing stability for potential therapeutic use, though delivery to cells remains a challenge.

Compared with protein enzymes, DNAzymes are easier to synthesize and modify, but they face obstacles such as limited catalytic efficiency under physiological conditions and potential off-target effects. Research continues to improve catalytic efficiency, specificity, and delivery, aiming to translate DNAzymes into clinical and industrial tools.