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PAP-A has an actual analytical selectivity of 104∼105 because of polymerase misincorporation within the extension product from the opposite primer (bypass reaction) [7].
Bi-directional PAP-A (Bi-PAP-A) was developed to eliminate the bypass reaction, and thereby increase analytical selectivity, by using two blocked primers that overlap at one base [8], [9] (Fig. S1B).
The full bypass reaction requires yeast polζ (Johnson et al, 2001).
In contrast, the ring-closed PdG adduct is a strong block for both sequential steps of the bypass reaction.
This notion, specifically regarding the extension step of the bypass reaction, is consistent with studies showing that in duplex DNA at neutral pH the aldehydic form predominated (52).
Additionally, low P treatment was characterized by transcriptional up-regulation of AOX (Additional file 4: Table S3), a bypass reaction to the oxidative phosphorylation [ 65].
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For instance, some complete bypass reactions involve the replicative enzymes polδ or polɛ (McCulloch et al, 2004).
The Qo site architecture formed by cyt b and Rieske iron sulfur protein (ISP) impedes harmful bypass reactions.
Particularly strong reaction to all three stress conditions was observed for two transcripts representing glycolytic bypass reactions, a PPi-dependent phosphofructokinase (GRMZM2G059151) and housekeeping PEPC (GRMZM2G110714).
Therefore, it would be advisable to constrain the fluxes through the bypass reactions to zero when specifically studying the wild-type network.
This is in line with the hypothesis that a distinct Qo motif is used in a specific redox system as to minimize bypass reactions of quinol oxidation.
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