Development of a fluorescence resonance energy transfer assay for measuring the activity of Streptococcus pneumoniae DNA ligase, an enzyme essential for DNA replication, repair, and recombination

Abstract

DNA ligase is an enzyme essential for DNA replication, repair, and recombination in all organisms. Bacterial DNA ligases catalyze a NAD +-dependent DNA ligation reaction, i.e., the formation of a phosphodiester bond between adjacent 3 ′-OH and 5 ′-phosphate termini of dsDNA. Due to their essential nature, unique cofactor requirement, and widespread existence in nature, bacterial DNA ligases appear to be valuable targets for identifying novel antibacterial agents. To explore bacterial DNA ligases as antibacterial targets and further characterize them, we developed a simple, robust, homogeneous time-resolved fluorescence resonance energy transfer assay (TR-FRET) for measuring Streptococcus pneumoniae DNA ligase activity. This assay involves the use of one dsDNA molecule labeled with biotin and another dsDNA molecule labeled with Cy5, an acceptor fluorophore. During ligation reactions, the donor fluorophore europium (Eu 3+) labeled with streptavidin was added to the assay mixtures, which bound to the biotin label on the ligated products. This in turn resulted in the FRET from Eu 3+ to Cy5 due to their close proximity. The formation of ligation products was measured by monitoring the emission at 665 nm. This assay was validated by the experiments showing that the DNA ligase activity required NAD + and MgCl 2, and was inhibited by NMN and AMP, products of the ligase reaction. Using this assay, we determined the K m values of the enzyme for dsDNA substrates and NAD +, and the IC 50 values of NMN and AMP, examined the effects of MgCl 2 and PEG 8000 on the enzyme activity, optimized the concentrations of Eu 3+ in the assay, and validated its utilities for high-throughput screening and biochemical characterizations of this class of enzymes.