= Deoxyribozyme
{wiki}
= DNAzyme
{c}
{synonym}
A \b[deoxyribozyme], or <DNAzyme>, is a <DNA> molecule with catalytic activity. Its <nucleotide sequence> permits a functional folded structure that accelerates a specified <chemical reaction>. Catalytic function is distinct from merely recognizing or binding a target, as an <aptamer> can do. The term identifies the catalytic material; it does not imply that every <DNAzyme> catalyzes the same reaction.
A motivating primary experiment by <Ronald R. Breaker> and <Gerald F. Joyce> selected DNA molecules that promoted cleavage of an <RNA> linkage. Their 1994 paper started with a large randomized DNA population and used repeated selection and amplification to enrich activity. The selected catalyst required lead ions under the tested conditions, and an intermolecular version achieved repeated substrate turnover. This established catalytic DNA in a laboratory selection system, rather than demonstrating a naturally occurring cellular enzyme.<A DNA enzyme that cleaves RNA by Ronald R. Breaker and Gerald F. Joyce>[Abstract, Background, Results and Conclusions]{ref}
A <DNAzyme turnover experiment> can distinguish a catalyst from a one-use reagent. For a constructed molecular count, suppose a preparation contains $10\,\mathrm{nM}$ active DNA catalyst and produces $100\,\mathrm{nM}$ specifically cleaved product. The ratio
$$
N_{\rm turnover}=\frac{[\text{product}]}{[\text{active catalyst}]}=10
$$
means ten reactions per active catalyst molecule on average. This interpretation requires controls for uncatalyzed product formation and an appropriate count of active molecules. The ratio alone gives neither a reaction rate nor a <turnover number> per unit time.
A time-resolved experiment additionally measures initial reaction rates while varying substrate concentration and holding other conditions fixed. A selected sequence, its inactive or altered controls and a substrate-only reference answer different questions about sequence dependence and background cleavage. <Yingfu Li> and <Ronald R. Breaker>'s primary measurements of chemically driven <RNA degradation> illustrate why that baseline matters when quantifying catalytic enhancement.<Kinetics of RNA Degradation by Specific Base Catalysis of Transesterification Involving the 2′-Hydroxyl Group by Yingfu Li and Ronald R. Breaker>[Abstract: defined substrates and background cleavage mechanism]{ref}
A catalyst changes the rate of approach to a chemical equilibrium without supplying unlimited chemical free energy. Its performance depends on folding, molecular recognition, reaction chemistry and product release; observing binding alone does not establish all of these functions.
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