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. 2006 Nov 8;5(11):1373-83.
doi: 10.1016/j.dnarep.2006.06.003. Epub 2006 Jul 28.

Multiple solutions to inefficient lesion bypass by T7 DNA polymerase

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Multiple solutions to inefficient lesion bypass by T7 DNA polymerase

Scott D McCulloch et al. DNA Repair (Amst). .

V体育ios版 - Abstract

We hypothesize that enzymatic switching during translesion synthesis (TLS) to relieve stalled replication forks occurs during transitions from preferential to disfavored use of damaged primer-templates, and that the polymerase or 3'-exonuclease used for each successive nucleotide incorporated is the one whose properties result in the highest efficiency and the highest fidelity of bypass. Testing this hypothesis requires quantitative determination of the relative lesion bypass ability of both TLS polymerases and major replicative polymerases. As a model of the latter, here we measure the efficiency and fidelity of cis-syn TT dimer and abasic site bypass using the structurally well-characterized T7 DNA polymerase. No bypass of either lesion occurred during a single round of synthesis, and the exonuclease activity of wild-type T7 DNA polymerase was critical in preventing TLS. When repetitive cycling of the exonuclease-deficient enzyme was allowed, limited bypass did occur but hundreds to thousands of cycles were required to achieve even a single bypass event. Analysis of TLS fidelity indicated that these rare bypass events involved rearrangements of the template and primer strands, insertions opposite the lesion, and combinations of these events, with the choice among these strongly depending on the sequence context of the lesion VSports手机版. Moreover, the presence of a lesion affected the fidelity of copying adjacent undamaged template bases, even when lesion bypass itself was correct. The results also indicate that a TT dimer presents a different type of block to the polymerase than an abasic site, even though both lesions are extremely potent blocks to processive synthesis. The approaches used here to quantify the efficiency and fidelity of TLS can be applied to other polymerase-lesion combinations, to provide guidance as to which of many possible polymerases is most likely to bypass various lesions in biological contexts. .

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Fig. 1
Fig. 1
Effects of a TT dimer and abasic site on T7 DNA polymerase processive synthesis. (A) Schematic representation of substrates used. The 20-mer primer (LBP-20) was 5′ end-labeled with 32P (*) and annealed to the template 45-mers shown. The upside down caret (v) denotes the position of the cissyn TT dimer. Tetrahydrofuran residue (X) mimics an abasic site. The underlined bases are the amber codon in the lacZα sequence. (B) Exonuclease-proficient (Exo+) T7 DNA polymerase reactions. Single hit reactions were performed using a 400-fold excess of substrate over enzyme. Reactions were performed for 0, 3, 6, 9 and 12 min and the products separated by 12% denaturing PAGE. The 0 and 6 min timepoints for each reaction are shown. A star (*) indicates the positions of the damaged bases for each substrate. A partial template sequence is given to the left of the gel. (C) Exonuclease-deficient (Exo) T7 DNA polymerase reactions. The details are the same as described for panel B. (D) Exonuclease-deficient (Exo) T7 DNA polymerase reactions using a two-fold excess of enzyme over substrate, incubated for 60 min. Full length (FL), −1, and +1 complete extension products are indicated on the left. Brackets on the right highlight the differences in both complete (upper bracket) and incomplete (lower bracket) bypass reactions for the different substrates. Reactions performed under these conditions using exonuclease-proficient enzyme display complete loss of signal, indicating degradation of the primer strand (data not shown).
Fig. 2
Fig. 2
Termination probability of T7 DNA polymerase on TT dimer and abasic site template DNA. Quantitative analysis of all time points from reactions depicted in panels A and B in Fig. 1 was used to determine the termination probability at each template position for undamaged (white) and lesion containing DNA (black). Termination probability, a measure of how much of a given size primer is further extended to longer product, is calculated as the pixel intensity of a given band, divided by the total pixel intensity of all bands that size and larger. Values plotted are the average of eight data points (four time points each for two repeat experiments). Error bars represent the standard deviation.

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