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A 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.^[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 ratiomeans 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.^[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.

RNA degradation is the chemical or enzymatic breakdown of RNA, including cleavage of its phosphodiester bonds into shorter strands. Fragmentation can remove the continuity needed for an RNA molecule's function even while much of its nucleotide sequence remains present. Ribonucleases catalyze RNA cleavage; chemical cleavage also occurs without an enzyme.

A chemical route exploits the hydroxyl group at the $2^{\prime }$ position of ribose. Its oxygen can act as a nucleophile toward the adjacent backbone phosphorus, producing an internal transesterification that breaks the chain. In their 1999 primary study, Yingfu Li and Ronald R. Breaker used chimeric DNA/RNA substrates to measure hydroxide-dependent cleavage of RNA phosphodiester bonds. Such a substrate isolates a susceptible linkage within a defined molecular context, allowing chemical instability to be measured separately from a complex sample's overall fragmentation pattern.^[ref]

An illustrative kinetic model follows the number $N$ of molecules that remain intact under constant conditions. If each intact molecule has a constant probability per unit time $k$ of undergoing its first destructive cleavage, thenThe last quantity is an RNA half-life in this model. With stipulated $k=0.020\mathrm{mi}{\mathrm{n}}^{-1}$, half the starting molecules remain intact after about $34.7\min$, and $e^{-1.2}\approx 30.1\%$ after an hour. The numerical rate is an example, not a universal value for RNA or a measurement from the cited experiment.

A cleavage need not remove material from the tube: breaking one long RNA into two pieces initially preserves its total number of nucleotides. Consequently a concentration measurement can stay almost unchanged while RNA integrity declines. An electropherogram can reveal redistribution toward shorter fragments, while a short target region may remain detectable by reverse transcription and polymerase chain reaction. The relevant question is which molecular continuity the intended assay requires.

Ronald R. Breaker is a biochemist at Yale University whose research investigates catalytic and regulatory functions of nucleic acids. His university biography connects his laboratory's work on deoxyribozymes with its investigations of riboswitches, in which RNA recognizes a molecular signal and affects gene expression.^[ref]

In the 1994 primary paper with Gerald F. Joyce, Breaker reported a DNA catalyst that cleaves an RNA linkage. The experiment used in vitro selection: molecules with useful activity were enriched through successive selection and amplification rounds. The selected chemistry depended on lead ions, so the result established catalytic capacity under the tested conditions, not the existence of a natural cellular DNA enzyme.^[ref]

The paper's intermolecular catalyst had a reported turnover number of about $1\mathrm{mi}{\mathrm{n}}^{-1}$. An original counting example explains the term: if $2\mathrm{nmol}$ of active catalyst each process one substrate per minute under sustained substrate-saturating conditions, the initial production rate is approximately $2nmol/min$. The catalyst can process more than its own molecular count over successive cycles. This differs from a reagent consumed once per cleavage. Binding, chemical reaction and product release can impose different kinetic limits.

Breaker later coauthored with Yingfu Li the primary study of chemically driven RNA degradation. That work supplies a baseline for interpreting catalysis: an apparent rate enhancement must compare a catalyzed reaction with the appropriate uncatalyzed reaction under specified conditions.^[ref]