The 3' end of the primer is the one that will grow by Taq polymerase during the PCR reaction. It needs to be a perfect match for both specificity and to prime the reaction properly.
A quick search found these pages: http://en.wikipedia.org/wiki/Polymerase_chain_reaction http://www.premierbiosoft.com/tech_notes/PCR_Primer_Design.html On 08/02/10 09:51, Gregory Dougherty wrote: > I understand why gfServer requires a perfect match for tileSize + stepSize - > 1 bases. But when looking for primers, why does the perfect match have to be at the 3' end, rather than any place else in the primer? (Or is the usage information for gfPcr incorrect?) > > TIA, > > Greg > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
