Polymerase chain reaction optimization: Difference between revisions

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== Hairpins ==

[[Secondary structure]]s in the DNA can result in folding or knotting of DNA template or primers, leading to decreased product yield or failure of the reaction. [[Stem-loop|Hairpin]]s, which consist of internal folds caused by base-pairing between nucleotides inis inverted repeats within single-stranded DNA, are common secondary structures and may result in failed PCRs.

Typically, primer design that includes a check for potential secondary structures in the primers, or addition of [[Dimethyl sulphoxide|DMSO]] or [[glycerol]] to the PCR to minimize secondary structures in the DNA template<ref>{{Cite web|url = https://www.neb.com/products/pcr-polymerases-and-amplification-technologies/taq-dna-polymerases/~/media/26059D85ADCD473DB16C5500AD69EE60.ashx|title = FAQs for Polymerases and Amplification|date = |accessdate = |website = |publisher = New England Biolabs}}</ref> {{Citation needed|date=February 2007}}, are used in the optimization of PCRs that have a history of failure due to suspected DNA hairpins.