Primer Design Survey

Wilson Clements kendrick at
Thu Sep 21 16:34:25 EST 2000


    I do a fair amount of RT-PCR and have designed primers for about ten to
15 genes.  I recommend the website for Primer3
(  My
experience with primers designed on this website is that I can get primers
that amplify a 200bp piece of my cDNA under very similar conditions (i.e.
the same Tm and number of amplification cycles), which is ideal for
amplifying a battery of genes.  The site allows for inputting many different
parameters.  I usually try to have a GC clamp of 2bps and look for pieces
that are not extremely far from the 3' end of the gene's coding region.

Wilson Clements    
Department of Biochemistry
University of Washington.

> From: richards-4 at medctr.osu.EDU (sam richards)
> Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre
> Newsgroups: bionet.molbio.methds-reagnts
> Date: 12 Sep 2000 14:31:04 +0100
> Subject: Primer Design Survey
> To All,
> I would like to survey all those who do PCR and sequencing primer
> design. I am gathering information for a workshop and would like to know
> what you think about primer design so I can put together a consensus of
> information.  Please take a few minutes and respond to this survey.
> Thank you for your time.
> Sam Richards
> Ohio State University
> Survey:
> 1. What guidelines do you use in designing primers?
> 2. How do you prefer designing primers (i.e. do you use software,
> website, or do you eye-ball it)?
> 3. If you use a website; which one do you use?
> 4. If you use a software package; which one is it?
> 5. Are there other design programs that you have used?
> 6. Is there any additional information that you would like to give about
> primer design that is not covered in this survey?
> ---

More information about the Methods mailing list