figure out the size of amplicon using known primer - (Dec/20/2007 )
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 http://genome.ucsc.edu/cgi-bin/hgPcr?db=hg17
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.