From The School of Biomedical Sciences Wiki
- Ideally primers should be 18-20 base pairs in length, this is so that they are unique enough to anneal to the DNA at the flanking sequences of the fragment/gene we wish to amplify or isolate and so that they anneal to the DNA after it has been melted before the rest of the strands re-anneal. they are also kept at this length to ensure that they do not "mis-prime" if 1 out of the 20 bases does not bind then polymerase will not be able to synthesize new DNA."
- Primers also cannot be complementary to each other, if so these form "primer dimers". this is when they anneal and are amplified instead of the intended DNA sample.
- Primers can also contain "dangling ends" these are restriction endonuclease sites at the outside edges of the primers that enable the DNA to be amplified to be inserted into a plasmid or genome cut by the same restriction endonuclease.
- Bases T and A should be avoided at the 3' end of the primer (as this is where polymerase binds) as they are more likely to mispair. G and C are much more stable.
- Primers can be modified to contain fluorophores so that when they bind to target sequences of DNA we can visualize and isolate them etc.