Limitations of PCR
There are some drawbacks of using PCR that one should be aware of as well. First, the sequence of the gene or chromosome region being targeted is required. This limitation is rapidly diminishing as gene and genome sequencing technology and sharing of this sequence through Internet data bases has emerged as the norm in genetic analysis. Because of the size of the genomes of living things and a high conservation of gene sequences in many organisms, primers designed for a PCR test must be empirically tested with the proper controls. Biologists can easily generate false positive DNA from PCR that is caused by contamination or lack of specificity in primer design. There may also be a need to optimize concentrations of each chemical component. For example, changing the amount of DNA template, or changing the conditions that influence Taq polymerase activity such as MgCl2 concentration can affect both the quantity and quality of DNA bands produced. Some studies have shown that even the brand of Taq polymerase can affect results. Likewise, the temperature cycles may need to be fine-tuned for a specific PCR test. Finally, as an in vitro DNA replication method, PCR cannot replicate entire chromosomes.