2006 )

hello everyone

i have not been here for a long time.
recently i will do some experiment related chromatin immunoprecipitation.
and the designation of the primer is a important part in the experiment
is there anyone who can tell me some experience on your primer design

hope for your suggestion

-Saturn100-

I alaways follow the guidelines on the Applied biosystems website!

-Raffaela-

For ChIP PCR priemr design, first rules for regular genomic DNA PCR should be followed.

Besides that, ChIP PCR has something special:

Usually focus is on a gene's promoter region which is mostly GC rich
To achieve high resolution, PCR product size should not be too big

Here are some general rules for designing ChIP primers:

Primers should have a size of 20-24mer

Primers should have a Tm of 58-60C

GC content of 40-70%

Avoid runs of an identical nucleotide (such as 'CCCC'), especially 'G's

Keep amplified fragments between 150-250 bp

Do a In-Silico PCR search or blast search make sure they amplify unique genomic region
First test your primers on genomic DNA.
Design at least 2 pairs of primers for each region of interest in case that some do not work

Hope that helps.

-pcrman-