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E. coli DNA polymerase III holoenzyme can form an initiation complex with a primed-DNA template by using ATPYS with an efficiency of approximately half that observed with ATP. After complex formation on singly primed poly(dA)5000, processive synthesis generates products thousands of nucleotides long, with a size distribution identical to that observed with ATP or excess P subunit. Increased salt concentration decreases the efficiency of complex formation more in the presence of ATPYS than ATP. However, the capacity of increased salt to lower the length of processive synthesis is the same in both cases. Stationary complexes dissociate more rapidly if formed by ATPYS versus ATP or excess R subunit. This instability is observed with complexes formed before initiation of DNA synthesis, with complexes stalled by encountering with primers, or with complexes terminated after dideoxynucleotide incorporation. When reactions containing mixtures of ATP and ATPYS, or excess 0 and ATPYS are examined the effects of ATP or excess 0 are dominant. Overall, these results indicate that neither ATP nor ATPYS specifically destabilize the complex after a period of synthesis. Rather, the complex formed by ATPYS is less stable throughout its lifetime. A possible reason is that ATPYS may induce complexes on only one side of an asymmetric dimeric DNA polymerase, a side that forms relatively weak complexes. ATP or R may induce complexes from both sides, such that average complex stability is higher.
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