PCR reaction - quick question! - (Apr/23/2008 )
Hello,
Please can anyone help answer what I hope is not so silly a question!
I was just wondering, in a typical PCR reaction profile ([DNA formed] vs. cycle number), I understand the exponential phase and plateau afterwards, but why is there an initial lag phase?
I can think of a few reasons.
When the template concentration is very low (unamplified) the chance is reduced for primers finding binding sites during the hybridization time.
When to-be amplified region represents a very low percent of template DNA, primers may unproductively hybridize with the similar but not completly complemntary DNA. And finally, in the initial rounds of the reaction a greater percentage of each primer extension reaction will be preformed on original unamplified template, so 3' end won't have been defined by other primer.
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When the template concentration is very low (unamplified) the chance is reduced for primers finding binding sites during the hybridization time.
When to-be amplified region represents a very low percent of template DNA, primers may unproductively hybridize with the similar but not completly complemntary DNA. And finally, in the initial rounds of the reaction a greater percentage of each primer extension reaction will be preformed on original unamplified template, so 3' end won't have been defined by other primer.
d
Brillaint! That makes perfect sense, I just realised (after years of doing PCR) of my complete ignorance of this feature of PCR reactions.
Thanks very much for your help, its much appreciated