Structural basis for the selective incorporation of an artificial nucleotide opposite a DNA adduct by a DNA polymerase.

The possibility to sequence cytotoxic O6-alkylG DNA adducts would greatly benefit research. Recently we reported a benzimidazole-derived nucleotide that is selectively incorporated opposite the damaged site by a mutated DNA polymerase. Here we provide the structural basis for this reaction which may spur future developments in DNA damage sequencing.

Data in support of quantification of pyrophosphate as a universal approach to determine polymerase activity and assay polymerase inhibitors.

Characterization of synthetic oligonucleotides and quantification of primer extension mediated by a human translesion synthesis polymerase η (Pol η) over drug-induced DNA lesions in the presence on modified nucleotide analogs is described. Extent of primer extension for each reaction was monitored by denaturing gel electrophoresis. The data was obtained to assess the performance of the fluorescence-based primer extension (PE-PiPer) assay [1] with respect to the established and conventionally used denaturing gel electrophoresis. The obtained data reflects the specific inhibition of translesion synthesis over cisplatin containing DNA with 5-OH-CTP.

Quantification of pyrophosphate as a universal approach to determine polymerase activity and assay polymerase inhibitors.

The importance of DNA polymerases in biology and biotechnology, and their recognition as potential therapeutic targets, drives development of methods for deriving kinetic characteristics of polymerases and their propensity to perform polynucleotide synthesis over modified DNA templates. Among various polymerases, translesion synthesis (TLS) polymerases enable cells to avoid the cytotoxic stalling of replicative DNA polymerases at chemotherapy-induced DNA lesions, thereby leading to drug resistance. Identification of TLS inhibitors to overcome drug-resistance necessitates the development of appropriate high-throughput assays. Since polymerase-mediated DNA synthesis involves the release of inorganic pyrophosphate (PPi), we established a universal and fast method for monitoring the progress of DNA polymerases based on the quantification of PPi with a fluorescence-based assay that we coupled to in vitro primer extension reactions. The established assay has a nanomolar detection limit in PPi and enables the evaluation of single nucleotide incorporation and DNA synthesis progression kinetics. The results demonstrated that the developed assay is a reliable method for monitoring TLS and identifying nucleoside and nucleotide-based TLS inhibitors.