What phase of PCR is analyzed for standard PCR?

In standard PCR (Polymerase Chain Reaction), the phase that is primarily analyzed is the exponential phase. This is the stage where the amplicons are generated at a rate proportional to the number of PCR cycles, leading to a doubling of the product with each cycle, assuming optimal conditions. During this phase, the number of target DNA molecules effectively doubles with each cycle, making it the most suitable time for quantification and analysis because the reaction is highly efficient and linear.

While it is common to refer to this stage as the exponential or log phase, in the context of PCR, the term "log phase" typically refers to the portion of the graph where amplification is progressing rapidly. The focus on exponential growth during PCR means that analyzed data often comes from this section, as it yields quantifiable results with a strong correlation to the initial amount of template DNA.

In contrast, the stationary phase occurs when the reaction components (like template DNA and primers) begin to get depleted, which causes a plateau effect and less reliable data. The declining phase indicates a drop-off in the amount of amplifiable product, as the reaction reaches its limits. Understanding these phases is crucial for optimizing PCR conditions and accurately interpreting results.