During Quick change SDM F and R primers are complementary of each other when performing independent Forward and reverse primer PCR reaction (In different tubes) for quick change SDM then it is Linear amplification.
During inverse PCR SDM F and R primers are designed back to back orientation and both primers are using in the same reaction (same tube) then it is exponential amplification.
Kindly explain exponential and linear amplification with respect to both kind of mutagenesis strategy?
The basic procedure requires the synthesis of a short DNA primer. This synthetic primer containing the desired mutation is complementary to the template DNA around the mutation site so it can hybridize with the DNA in the gene of interest.. The single-strand primer is then extended using a DNA polymerase, which copies the rest of the gene. The copied gene contains the mutated site, and is then introduced into a host cell as a vector and cloned.
Quickchange (Stratagene) two complementary oligos containing the desired mutation are used to prime extensions all the way around the plasmid. The product of the reaction is never used as a template. Quickchange is a linear amplification and each round of extensions is performed on the plasmid template.
As Caroline Waters mentioned, your PCR amplifications of any senses using the primers designed by standard SDM (Quickchange, Stratagene) are just primer extensions without any exponential amplification. The reason is that all your PCR products cannot be used as the templates for the sequential cycle of PCR amplification (exponential amplification needs the PCR products as the templates for the sequential PCR cycles), and in each PCR cycle, your primers are just annealed to your original templates (plasmid DNA) to synthesis the DNA fragment with a length depending on your extension time. You can get more explanation on http://bmcbiotechnol.biomedcentral.com/articles/10.1186/1472-6750-8-91.
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