Mechanistic Insights into Replication Across from Bulky DNA Adducts: A Mutant Polymerase I Allows an N-Acetyl-2-aminofluorene Adduct To Be Accommodated during DNA Synthesis

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Abstract
The molecular mechanism that allows a polymerase to incorporate a nucleotide opposite a DNA lesion is not well-understood. One way to study this process is to characterize the altered molecular interactions that occur between the polymerase and a damaged template. Prior studies have determined the polymerase−template dissociation constants and used kinetic analyses and a protease digestion assay to measure the effect of various DNA adducts positioned in the active site of Klenow fragment (KF). Here, a mutator polymerase was used in which the tyrosine at position 766 of the KF has been replaced with a serine. This position is located at the junction of the fingers and palm domain and is thought to be involved in maintaining the active site geometry. The primer-template was modified with N-acetyl-2-aminofluorene (AAF), a well-studied carcinogenic adduct. The mutant polymerase displayed a significant increase in the rate of incorporation of the correct nucleotide opposite the adduct but was much less prone to incorporate an incorrect nucleotide relative to the wild-type polymerase. Both the wild-type and the mutant polymerase bound much more tightly to the AAF-modified primer-template; however, unlike the wild-type polymerase, the binding strength of the mutant was influenced by the presence of a dNTP. Moreover, the mutant polymerase was able to undergo a dNTP-induced conformational change when the AAF adduct was positioned in the active site, while the wild-type enzyme could not. A model is proposed in which the looser active site of the mutant is able to better accommodate the AAF adduct.