= DNAzyme turnover experiment
{c}
A \b[DNAzyme turnover experiment] measures how much reaction product a <DNAzyme> forms over time relative to the amount of active catalyst. Its central distinction is between one productive event per catalyst molecule and repeated substrate processing. The original <deoxyribozyme> paper reported an intermolecular catalyst with repeated turnover, rather than merely stable binding to its target.<A DNA enzyme that cleaves RNA by Ronald R. Breaker and Gerald F. Joyce>[Abstract, Results: intermolecular catalytic activity and turnover]{ref}
The observable should be chemically identified product, for example a resolved cleavage product quantified from an appropriately calibrated <gel electrophoresis> signal. Record a time course and distinguish the catalyst-dependent contribution from initial product and substrate-only background. An altered-sequence control tests sequence dependence; it does not automatically replace a measurement of background chemistry.
For a constructed example, suppose the initial substrate concentration is $200\,\mathrm{nM}$ and active catalyst concentration is $5\,\mathrm{nM}$. Background-corrected product reaches $40\,\mathrm{nM}$ after 20 minutes. Then
$$
N_{\rm turnover}=\frac{40}{5}=8,\qquad
\overline r_{\rm turnover}=\frac{8}{20\,\mathrm{min}}=0.40\,\mathrm{min^{-1}}.
$$
The first is a dimensionless cumulative count; the second is an interval-average rate. Neither is automatically the <turnover number> at saturating substrate. Substrate depletion, changes in active catalyst and product inhibition can make the time course nonlinear.
A rapid initial product burst followed by a slower nearly linear phase can indicate different kinetic stages. For illustration,
$$
P(t)=A(1-e^{-k_b t})+v_{\rm ss}t
$$
contains a burst amplitude $A$ and later slope $v_{\rm ss}$. Such a curve motivates investigating <DNAzyme product-release limitation>, but does not uniquely prove that mechanism: catalyst heterogeneity or inactivation can also alter the trace. Independent perturbations and product-release observations are needed to distinguish explanations.
A background reference matters especially when the substrate can cleave chemically without the DNAzyme. The primary analysis of chemically driven <RNA degradation> provides the relevant distinction between baseline cleavage and 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: background cleavage and interpretation of rate enhancement]{ref}
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