Since the presence of secondary structures in primers and also DNA template has detrimental effects in PCR reactions, I was using the web tool http://www.idtdna.com/analyzer/Applications/OligoAnalyzer/ to test the probable DNA template self dimer formation and their dG. However I couldn't find information about the limit of permissible value of those dG, in order to be sure that primer-template annealing is more stable than template-template self dimer. Does anyone have some suggestions?
dG values though important are not the only factors you should consider, the position of the dimer is also important, a 3' dimer is much more detrimental than a 5' dimer. Also a lot depends on the melting temperature of the primer. In general it is recommended that a primer dimer should not have a dG value lower than -6, the closer to zero the better. Primers with higher melting temperatures can tolerate more.
Try to play with this:
http://yellow.nist.gov:8444/dnaAnalysis/primerToolsPage.do
J.
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