Failed polymerase chain reactions (PCRs) are a common cause of frustration in the lab. While a typical PCR protocol is quite straightforward, scientists must optimize each step to amplify the intended DNA fragment.
To develop a successful PCR protocol, scientists can change a multitude of factors. First, they must
identify the ideal temperature and cycle time for primer annealing. To do this, a scientist repeats their PCR reaction multiple times to change the annealing temperature or time while keeping all other variables constant. This optimization process can be quite time-consuming, but modern thermal cyclers have incorporated a gradient technology that significantly accelerates optimization by allowing scientists to change the annealing temperature for each reaction across the width of a thermal block.
A second step that benefits from a gradient PCR is DNA denaturation. Scientists rarely consider suboptimal denaturation conditions as a cause of low PCR yields. However, while the majority ...
