Stopped-flow DNA polymerase assay by continuous monitoring of dNTP incorporation by fluorescence

Abstract

DNA polymerase activity was measured by a stopped-flow assay that monitors polymerase extension using an intercalating dye. Double-stranded DNA formation during extension of a hairpin substrate was monitored at 75°C for 2min. Rates were determined in nucleotides per second per molecule of polymerase (nt/s) and were linear with time and polymerase concentration from 1 to 50nM. The concentrations of 15 available polymerases were quantified and their extension rates determined in 50mM Tris, pH 8.3, 0.5mg/ml BSA, 2mM MgCl2, and 200μM each dNTP as well as their commercially recommended buffers. Native Taq polymerases had similar extension rates of 10–45nt/s. Three alternative polymerases showed faster speeds, including KOD (76nt/s), Klentaq I (101nt/s), and KAPA2G (155nt/s). Fusion polymerases including Herculase II and Phusion were relatively slow (3–13nt/s). The pH optimum for Klentaq extension was between 8.5 and 8.7 with no effect of Tris concentration. Activity was directly correlated to the MgCl2 concentration and inversely correlated to the KCl concentration. This continuous assay is relevant to PCR and provides accurate measurement of polymerase activity using a defined template without the need of radiolabeled substrates.