The ability of a variety of polymerases to synthesize past site-specific cis-syn, trans-syn-II, (6-4), and Dewar photoproducts of thymidylyl- (3→5')- thymidine

The role of photoproduct structure, 3' → 5' exonuclease activity, and processivity on polynucleotide synthesis past photoproducts of thymidylyl- (3' → 5')-thymidine was investigated. Both Moloney murine leukemia virus reverse transcriptase and 3' → 5' exonuclease-deficient (exo^-) Vent polymerase were blocked by all photoproducts, whereas Taq polymerase could slowly bypass the cis-syn dimer. T7 RNA polymerase was able to bypass all the photoproducts in the order cis-syn > Dewar > (6-4) > trans-syn-II. Klenow fragment could not bypass any of the photoproducts, but an exo^- mutant could bypass the cis-syn dimer to a greater extent than the others. Likewise T7 DNA polymerase, composed of the T7 gene 5 protein and Escherichia coli thioredoxin, was blocked by all the photoproducts, but the exo^- mutant Sequenase 2.0 was able to bypass them all in the order cissyn > Dewar > trans-syn-II > (6-4). No bypass occurred with an exo^- gene 5 protein in the absence of the thioredoxin processivity factor. Bypass of the cis-syn and trans-syn-II products by Sequenase 2.0 was essentially non-mutagenic, whereas about 20% dTMP was inserted opposite the 5'-T of the Dewar photoproduct. A mechanism involving a transient abasic site is proposed to account for the preferential incorporation of dAMP opposite the 3'-T of the photoproducts.