DNA Polymerase β Gap-Filling Translesion DNA Synthesis

Although the primary function of DNA polymerase (pol) beta is associated with gap-filling DNA synthesis as part of the DNA base excision repair pathway, translesion synthesis activity has also been described. To further understand the potential role of pol beta-catalyzed translesion DNA synthesis (TLS) and the structure-function relationships of specific residues in pol beta, wild-type and selected mutants of pol beta were used in TLS assays with DNA substrates containing bulky polycyclic aromatic hydrocarbon-adducted oligonucleotides. Stereospecific (+) and (-)-anti-trans-(C10S and C10R) benzo[a]pyrene-7,8- dihydrodiol-9-10-epoxide (BPDE) adducts were covalently attached to both the N-6-adenine and N-2-guanine in the major and minor grooves, respectively. For all substrates tested, the presence of the BPDE adducts greatly decreased the efficiency of nucleotide incorporation opposite the lesion, and the stereochemistry of the adducts also further modulated the efficiency of the insertion step, such that lesions which were oriented in the 3' direction relative to the approaching polymerase were considerably more blocking than those oriented in the 5' direction. In the absence of a downstream DNA strand, the extension step beyond the adduct was extremely inefficient, relative to a dinucleotide gap-filling reaction, such that in the presence of the downstream DNA, dinucleotide incorporation was strongly favored. In general, analyses of the TLS activities of four pol beta mutants revealed similar overall properties, but wild-type pol beta exhibited more than 50-fold greater extension and bypass of the C10S-dA adducts as compared to a low fidelity mutant R283K expected to interact with the templating base. Replication bypass investigations were further extended to include analyses of HIV-1 reverse transcriptase, and these studies revealed patterns of inhibition very similar to that observed for pol beta.