Editing Polymerase chain reaction (section)

==Optimization==
{{Main|PCR optimization}}
In practice, PCR can fail for various reasons, such as sensitivity or contamination.<ref>{{cite journal|url=http://tools.thermofisher.com/Content/Focus/Focus%20Volume%2022%20Issue%201.pdf|archive-url=https://web.archive.org/web/20170307123818/http://tools.thermofisher.com/Content/Focus/Focus%20Volume%2022%20Issue%201.pdf|archive-date=2017-03-07|title=PCR from problematic templates|journal= Focus |volume=22|issue=1|pages=10 |year=2000|author1=Borman, Jon |author2=Schuster, David |author3=Li, Wu-bo |author4=Jessee, Joel |author5=Rashtchian, Ayoub }}</ref><ref>{{cite journal|url=http://tools.thermofisher.com/Content/Focus/Focus%20Volume%2022%20Issue%201.pdf|archive-url=https://web.archive.org/web/20170307123818/http://tools.thermofisher.com/Content/Focus/Focus%20Volume%2022%20Issue%201.pdf|archive-date=2017-03-07|title=Helpful tips for PCR|journal= Focus |volume=22|issue=1|pages=12 |year=2000|last1=Bogetto|first1=Prachi|last2=Waidne|first2=Lisa|first3=Holly|last3=Anderson}}</ref> '''Contamination''' with extraneous DNA can lead to spurious products and is addressed with lab protocols and procedures that separate pre-PCR mixtures from potential DNA contaminants.<ref name=molecular_cloning /> For instance, if DNA from a crime scene is analyzed, a single DNA molecule from lab personnel could be amplified and misguide the investigation. Hence the PCR-setup areas is separated from the analysis or purification of other PCR products, disposable plasticware used, and the work surface between reaction setups needs to be thoroughly cleaned.

'''Specificity''' can be adjusted by experimental conditions so that no spurious products are generated. Primer-design techniques are important in improving PCR product yield and in avoiding the formation of unspecific products. The usage of alternate buffer components or polymerase enzymes can help with amplification of long or otherwise problematic regions of DNA. For instance, Q5 polymerase is said to be ≈280 times less error-prone than Taq polymerase.<ref>{{Cite web|last=Biolabs|first=New England|title=Q5® High-Fidelity DNA Polymerase {{!}} NEB|url=https://www.neb.com/products/m0491-q5-high-fidelity-dna-polymerase#Product%20Information|access-date=2021-12-04|website=www.neb.com|language=en}}</ref><ref>{{Cite journal|last1=Sze|first1=Marc A.|last2=Schloss|first2=Patrick D.|title=The Impact of DNA Polymerase and Number of Rounds of Amplification in PCR on 16S rRNA Gene Sequence Data|journal=mSphere|year=2019|volume=4|issue=3|pages=e00163–19|doi=10.1128/mSphere.00163-19|pmc=6531881|pmid=31118299}}</ref> Both the running parameters (e.g. temperature and duration of cycles), or the addition of reagents, such as [[formamide]], may increase the specificity and yield of PCR.<ref>{{cite journal | vauthors = Sarkar G, Kapelner S, Sommer SS | title = Formamide can dramatically improve the specificity of PCR | journal = Nucleic Acids Research | volume = 18 | issue = 24 | pages = 7465 | date = December 1990 | pmid = 2259646 | pmc = 332902 | doi = 10.1093/nar/18.24.7465 }}</ref> Computer simulations of theoretical PCR results ([[In silico PCR|Electronic PCR]]) may be performed to assist in primer design.<ref name="ePCR">{{cite web|title=Electronic PCR|url=https://www.ncbi.nlm.nih.gov/sutils/e-pcr/|publisher=NCBI – National Center for Biotechnology Information|access-date=13 March 2012}}</ref>