Jeff Martino asked :
>In your opinion what's the best _commercial_ Macintosh program for
>PCR/sequencing primer design.
>Quote: "I want to enter a template sequence, show the acceptable region of
>the template I want the primer(s) to bind, and let the program choose the best
>primer or pair -- minimized secondary structure, minimized self-dimer,
>minimized dimer with other amplimer, etc."
>>Any and all comments on your experiences are appreciated.
We use here Oligo which was written by Wojciech Rychlik (Rychlic et al. 1990,
Nucleic Acids Res. 18, 6409-6412) and is commercialised by :
National Biosciences, Inc.
3650 Annapolis Lane
Plymouth, MN 55447
Tel (800) 747-4362 / (612) 550-2012
Fax (800) 369-5118 / (612) 550-9625
Distributor for Europe is :
Postboks 2640 St. Hanshaugen
N-0131 Oslo 1, Norway
Tel (47-2) 20 01 37
Fax (47-2) 20 01 89
A PC compatible version is also available.
When we purchased it (Feb 92) the price was US$640 for non profit organizations
and US$800 for industry.
I don't know if this is actually the best one since it's the only one I've
ever used on a Macintosh (has anyone heard of another one?... ) but it
certainly looks like one that might fit your requirements. You enter the
template sequence and specify the regions of acceptable primer annealing,
and you get a pair of oligos that fit the following requirements :
- no significant self-dimer
- no significant annealing between primers
- overall oligo stability
- 3'end stability
- unique 3'ends
- no homooligomers
- no harpins
Results include : Tm for selected primers, amplification product, optimal
annealing temperature, extinction coefficient of products...
One interesting feature of Oligo is that it calculates Tm of short sequences
with the nearest-neighbour method described by Breslauer et al. (1986 PNAS 83,
3746-3750) for DNA and Freier et al. (1986 PNAS 83,9373-9377) for RNA.
Furthermore, if you're not satisfied with the standard method you may conduct
the search in a totally personalised way.
Finally, Oligo can be used for designing oligos for other purposes than PCR
(sequencing, mutagenesis, hybridisation).
Well, all this would be perfectly allright without some little problems...
First of all, Oligo does not actually search (automatically speaking...) for
the best pair of oligos but for the FIRST pair of oligos it could find that
fit all requirements.
What's more, automatically selected primers cannot be of different size!!!
I can't think of anything else to say at the moment...
I hope this was of some help...
LGME du CNRS
11 rue Humann
67085 Strasbourg Cedex - FRANCE
Tel : (33) 88 37 12 55 #452
plewniak at titus.u-strasbg.fr