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The experiments of substrate specificity using several substrates were performed under multiple turnover conditions using 100 nM HDV ribozyme and 1 µM substrate.
The RNA was incubated with the purified archaeal exosome was incubated at 37°C under multiple turnover conditions (∼10 pmol enzyme, ∼40 pmol substrate) in a buffer containing 25 mM Tris-HCl pH 7.5, 100 mM NaCl, and10 mM inorganic phosphate (PO43−).
To demonstrate the phosphorylytic RNase activity in our purified archaeal exosome, we incubated the purified exosome with a 254-nt RNA substrate flanked by a strong 5'-tertiary RNA structure (the hepatitis delta virus ribozyme) and a 161-nt flexible 3' tail under multiple turnover conditions.
In vitro phosphorylation assays providing multiple turnover conditions were performed in a final volume of 25 µl of reaction buffer (50 mM Tris-HCl, pH 7.5, 50 mM KCl, 10 mM MgCl2, 0.5 mM ATP, 420 nM [γ33P]ATP (3000 Ci/mmol)).
This was in contrast to the narrower range observed under multiple turnover conditions (compare Figure 4A to 4E).
Under multiple turnover conditions, all proteins were active (except the R55K K225R mutant), but their pH optima differed.
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Under a multiple turnover condition, both performed well at 37°C, showing the kcat of 1 and 0.26 min−1, respectively.
Note that commercial T4 DNA ligase is purified in a preadenylated form [24]. Thus, while the complete reaction cycle requires ATP, the enzyme (4 µM) is in molar excess over the substrate (3.3 µM), and these reactions proceed under stoichiometric rather than multiple-turnover conditions.
Two different effects were observed under multiple-turnover conditions.
As one can see in Figure 7, under multiple-turnover conditions the progress curve of MtATP-PRT displays burst kinetics.
By monitoring transient kinetics under multiple-turnover conditions, one can often obtain kinetic information not available during steady-state measurements.
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