Hairpins
Secondary structures in the DNA can result in folding or knotting of DNA template or primers, leading to decreased product yield or failure of the reaction. Hairpins, which consist of internal folds caused by base-pairing between nucleotides in 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 DMSO or glycerol to the PCR to minimize secondary structures in the DNA template, are used in the optimization of PCRs that have a history of failure due to suspected DNA hairpins. http://www.promega.com/pnotes/65/6921_27/6921_27_core.pdf
Read more about this topic: Polymerase Chain Reaction Optimization
Famous quotes containing the word hairpins:
“I feel perfectly miserable with 19 hairpins all sticking straight into my head. But, dear me, let us be elegant or die!”
—Victor Heerman (1893–1977)