Microsatellite (SSR)- Agarose Gel or Polyacrylamide Gel

[dnamolecule]

Hello all!
I'm planning to do SSRs marker. Should I use 2% agarose gel to detect DNA fragments or should I use polyacrylamide (PAA).

Thanks in advance

[admin]

Hi there DNAmolecule!
Happy New Year!
If your difference in microsatellites is more (10-11 bp) you can use 3% agarose, but if it is less then do PAGE. Metaphor gel is also good to use. In pAGE the difference and ease to score is worth doing.

Hope this helped!
Cheers

[DaniloT]

Originally Posted by dnamolecule

Hello all!
I'm planning to do SSRs marker. Should I use 2% agarose gel to detect DNA fragments or should I use polyacrylamide (PAA).

Thanks in advance

We suggest you to use Elchrom Scientific gels which are not acrylamide but same resolution (up to 1 bp) and not toxic!!! For further information look at
Elchrom Scientific homepage (type the name in google)
where you can find also reference on Microsatellite.

[DaniloT]

Use Elchrom Scientific gels. Same resolution of acrylamide (up to 1 bp) but precast and not toxic!! Go to Elchrom Scientific homepage (via google) and look at the many references on Microsatellite.