Deoxyribozymes or DNA enzymes or catalytic DNA, or DNAzymes are DNA molecules with catalytic action. In contrast to a RNA ribozyme that has many catalytic capabilities, DNA is only associated with gene replication and nothing else. The reasons are that DNA lacks specific functional groups and that DNA prefers the double coil conformation in which potential catalytic sites are shielded. In comparison to proteins built up from 20 monomers both RNA and DNA have a much more restricted set of monomers (4) to choose from which limits the construction of interesting catalytic sites. For these reasons DNAzymes exist only in the laboratory.

The first deoxyribozyme was discovered in 1994 by current Yale Professor Ronald R. Breaker while a postdoctoral fellow in the laboratory of Prof. Gerald F. Joyce at The Scripps Research Institute in La Jolla, CA. This deoxyribozyme assists in lead ion dependent RNA cleaving operations. Catalytic amplification was found to be a 100 fold compared to the uncatalysed reaction. Many other deoxyribozymes have since been developed that catalyse DNA phosphorylation, DNA adenylation, DNA deglycosylation, porphyrin metalation, thymine dimer photoreversion and DNA cleavage. Of particular interest are DNA ligases . These molecules have demonstrated remarkable chemoselectivity in RNA branching reactions. Although each repeating unit in a RNA strand owns a free hydroxyl group, the DNA ligase takes just one of them as a branching starting point. An accomplishment unattainable with traditional organic chemistry. DNAzymes have found practical use in metal biosensors .

This link and this link describes the DNA molecule 5'-GGAGAACGCGAGGCAAGGCTGGGAGAAATGTGGATCACGATT-3' which acts as a deoxyribozyme that uses light to repair a thymine dimer, using serotonin as cofactor.

With the aid of combinatorial chemistry techniques it is possible to generate a great many DNA sequences (up to 10¹⁶ of them) in a single experiment with 20 to 200 base pairs each that can be screened for a specific catalytic task. In this way the sheer number of DNA candidates make up for the fact that DNA is actually more appropriate for information storage than for catalysis. An inherent disadvantage of DNA enzymes is product inhibition and single-turnover behavior. It may therefore be argued if DNA enzymes can be counted as true catalysts. On the other hand low catalytic turnover is observed with many natural (non-DNA) occurring enzymes. Although the discovery of RNA enzymes predates that of DNA enzymes the latter have some distinct advantages. DNA has better cost-effectiveness and DNA can be made with longer sequence length and can be made with higher purity in Solid-phase synthesis.

Chirality is another property that a DNAzyme can exploit. DNA occurs in nature as a right-handed double helix and in asymmetric synthesis a chiral catalyst is a valuable tool in the synthesis of chiral molecules from an achiral source. In one application an artificial DNA catalyst was prepared by attaching a copper ion to it through a spacer . The copper - DNA complex catalysed a Diels-Alder reaction in water between cyclopentadiene and an aza chalcone. The reaction products (endo and exo) were found to be present in an enantiomeric excess of 50%.

Other uses of DNA in chemistry are in DNA-templated synthesis, DNA nanowires and DNA computing .

References

• A DNA enzyme that cleaves RNA Ronald R. Breaker and Gerald F. Joyce Chemistry & Biology, 1, 223 Abstract
• Deoxyribozymes: DNA catalysts for bioorganic chemistry Scott K. Silverman Org. Biomol. Chem. 2004, 2, 2701-2706 Article
• Optimization of a Pb2+-Directed Gold Nanoparticle/DNAzyme Assembly and Its Application as a Colorimetric Biosensor for Pb2+ Juewen Liu and Yi Lu Chem. Mater. 2004, 16, 3231-3238 Article
• DNA-Based Asymmetric Catalysis Gerard Roelfes, Ben L. Feringa Angewandte Chemie International Edition page 3230 2005
• DNA as a Nanomaterial Yoshihiro Ito a, Eiichiro Fukusaki Journal of Molecular Catalysis B: Enzymatic 28 (2004) 155–166 article

DNA