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Deoxyribozymes or DNA enzymes or catalytic DNA, or DNAzymes are DNA molecules with catalytic action. In contrast to the 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 different 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 [1] by current Yale Professor Ronald R. Breaker while a postdoctoral fellow in the laboratory of Prof. Gerald 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 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.[2] 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.[3]
For example, the DNA molecule 5'-GGAGAACGCGAGGCAAGGCTGGGAGAAATGTGGATCACGATT-3' which acts as a deoxyribozyme that uses light to repair a thymine dimer, using serotonin as cofactor[4] .[5]
With the aid of combinatorial chemistry techniques a great many DNA sequences (up to 1016 of them) can be generated 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 DNA being 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.[6] 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%. Later it was found that an enantiomeric excess of 99% could be induced, and that both the rate and the enantioselectivity were related to the DNA sequence.
Other uses of DNA in chemistry are in DNA-templated synthesis, DNA nanowires and DNA computing.[7]