Notes about designing primers
2015-03-12azim58 - Notes about designing primers
Designing PCR Primers
Primer3 can be used to determine appropriate primers. Alternatively, you could use Primer-BLAST for Finding primers specific to your PCR template (using Primer3 and BLAST) (http://www.ncbi.nlm.nih.gov/tools/primer-blast/). You could also use the Harvard Primer databae if you think that primers for your DNA sequence of interest may already exist. It is also good to have a sequencing primer end in a C or G at the 3' end (a "GC clamp").
Primers are typically 18-22 bp long and should have a Tm in the 68-72 C range (52-58 C range according to Andrey's spreadsheet) with a GC content of 40-60%.
Primers should be about 100-200 bp upstream of the gene of interest (if the purpose is for sequencing).
One could also make sure that there are no hairpins in the primer with a Tm around the 52-58 C range. Hairpin Tms can be checked with a program such as Generunner (Analysis->Oligo).
see Andrey's preferred method for calculating Tm in CIM
CIM also has a program in the administration folder in the custom
software folder called Primer design plus
see Ordering Primer Form