RT-PCR - primer design (Jun/30/2002 )

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Primers are gene specific, not cell specific. If the primers you found in literature are for the gene your want to amplify, then you can use the primer. Alternative you can design your own primers. First you have to get the mRNA (or CDs, coding sequence in GenBank) sequence of your gene from Genbank. It's better to use RefSeq which is the most representative sequence in GenBank.  You can first go to LocusLink at http://www.ncbi.nlm.nih.gov/LocusLink/ to search your gene and find the right one of your organism, then under the section "NCBI Reference Sequences (RefSeq)", you will find the reference mRNA sequence. Once you have the sequence, you can, manually or with the help of primer design software,  design your primer. It's preferable that you know the gene structure (exons and introns) before designing your primers since it will be better to have your pcr product span some intron to discriminate DNA contamination. Anyway, for beginner, it's ok to use primers found in literature.

good luck.

(Edited by pcrman at 3:23 am on July 3, 2001)