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Using two primer sets, a-K474R and a-R476K, we observed PCR products and obtained transformants using the double primer protocol (with Pfu polymerase).
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We observed that widely used double-primer protocol resulted in insertion of multiple copies of primer probably due to primer-primer annealing.
In initial studies we used a double-primer PCR mutagenesis protocol, but sequencing of products showed tandem repeats of primer in cloned DNA.
To overcome the problem of primer-primer annealing observed with the double primer-procedure, we developed an alternative single-primer PCR procedure outlined in Figure 1.
We first tested this protocol using the same primer-sets that did not work with the double-primer method.
We start the single-primer PCR protocol with ~500 ng plasmid template that is about 10 times higher than that recommended for the double-primer PCR (Table 4) because, DNA amplification in the single-primer PCR is much lower (Table 4).
In SDM protocols that use forward and reverse primers with complementary sequences, primer-primer annealing can be a significant problem as we observed in our use of double-primer method.
Table 4 provides a list of the differences between the single-primer PCR and the double-primer PCR methods.
So far, we have not observed tandem repeats of a primer as we observed in the double-primer PCR method.
Table 4 summarizes the major differences in the initial stages of single-primer and double-primer PCR reactions.
A double injection protocol was used.
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