Biochemistry Questions / Explain the importance of designing primers that amplify a PCR product of approximately 400-600 bp in size in a PCR-based genotype screen.

PCR begins to loose accuracy with longer products. It is therefore undesired to have long PCR products, in excess of 600 bp.

This can be due to the DNA polymerase dissociating from the strand being amplified. On dissociation, the PCR product will not become longer, and may be of indeterminate length.

A PCR product of 400-600 bp is highly unlikely to have a similar sequence within a bacterial genome and therefore will likely amplify from a single locus. This allows for a successful genotype screen, allowing the identification of the genotype of interest and enabling the identification of successful (or unsuccessful) amplification by electrophoresis.