Protocol Online logo
Top : Forum Archives: : Molecular Biology

figure out the size of amplicon using known primer - (Dec/20/2007 )

Hi everyone,

one summer student of our lab did not finish his project and left two sets of lyophilized customer primer from invitrogen in the freezer without any document. right now I have to pick up his left over. my question:

1. ddH2o or TE buffer which one is better choice for reconstitution? is that true some of primer might include Tris and EDTA ingredient in and just simply add ddH2O( I am not sure)?

2. how do I know the size of PCR product it generated? what kind software I could use? NCBI blast tool ? I don't even know what gene Id he employed for primer design.

any input would be very appreciated.


These primers are pretty much wasted, unless you can get in touch with him/her directly. Can you read sequence on the labels? Some labs keep record of primers purchased, many dont.


you can do a blat search using the primer sequences
The results are matched genomic sequences. if the primers are for RT-PCR, you have to subtract the introns to get the right product size. If any of the primers spans an exon-exon junction, blat will not give results.

you can also do a ncbi blast search by putting the two primer sequences together with some "nnnn"s in between.

TE is more stable than water for reconstituting primers.


many thanks to pcrman and genehunter-1. I will try.