What is the primary purpose of using dUTP in PCR?

The use of dUTP in PCR serves a specific function that aligns closely with the need for differentiation of amplified products. When dUTP is incorporated into the PCR reaction, it can provide a mechanism for distinguishing between PCR products that contain dTTP and those that include dUTP. This is particularly valuable in situations such as cloning or in the presence of contamination, where identifying the original source of the PCR products is crucial.

When dUTP is used in conjunction with specialized enzymes like uracil-N-glycosylase (UNG), it allows for the selective degradation of PCR products that contain uracil, which is the result of dUTP incorporation. As a consequence, any residual products from previous reactions can be eliminated, thus preventing contamination in subsequent experiments. This ability to differentiate and selectively remove products is why the use of dUTP is favored for careful handling of amplified sequences, especially in diagnostic and research settings.

In contrast, while factors like enhancement of amplification speed, prevention of contamination, and increasing primer affinity are important aspects of PCR optimization, they do not directly pertain to the primary functional role that dUTP fulfills in allowing for the differentiation of amplified products.