Notes+about+designing+primers

Primer3 can be used to determine appropriate primers. 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 52-58 C range. Primers should be about 100-200 bp upstream of the gene of interest. 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 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