On the one hand, it is important that the reaction components hold the target temperatures of the cycles for a certain period of time in order to ensure an optimal, i.e. specific, PCR run with high yield. For example, the duration of the denaturation step depends on the GC-content and possible secondary structures of the target sequence, and the elongation time depends on the length of the target sequence. The number of cycles, on the other hand, is dictated by the copy number which enters into the reaction. Specific PCR reagents such as, for example, a modified polymerase that displays higher processivity, or additives that accelerate primer annealing or influence the melting behavior of the DNA, respectively, may help reduce the holding times required, and thus the duration of the run, especially in the case of long amplicons.
Since PCR consists of a large number of temperature changes, the speed at which the sample reaches the required temperature is also relevant. This speed is determined by three main factors: the thermocycler, the consumables and the sample volume. The speed is a direct result of the active heating and cooling capacity of the instrument in combination with the conductivity of the heating block. Silver, for example, displays higher thermal conductivity than aluminum (table 1), which affects the heating and cooling rates of cyclers with blocks made from the respective materials (figure 2).