Midiprep comparisons.. - Invitrogen vs. Qiagen (Jan/09/2008 )

Hi,
I am performing transient transfections of promoter-luciferase plasmids in numerous cell lines to compare promoter activity of various mutants using plasmids prepared with both Invitrogen's HiPure midi prep kit and also Qiagen's endo-toxin free midi-prep kit. Both claim to be endotoxin free, yet I am getting very different results when I transfect the same plasmid prepared by the two different methods. I nanodrop the both types of plasmid prep before transfection, and both types have 260/280 = 1.8-1.84 but vary in the 260/230 with Invitrogen preps around 2.45 and Qiagen preps at 2.2. I also have a higher yield for the Invitrogen preps.

I am trying to get a feeling for people's experience with either type of midi-prep. I get similar error between the two transfections, but the Invitrogen kit is showing me a very drastic reduction of promoter activity for one particular mutant whereas the Qiagen preps do not. I am also getting consistent results across cell lines with the Invitrogen kit, whereas I am not with the Qiagen kits.

Can anyone offer me advice on this?

use the one that gives you the best, most consistent results for your purposes (sounds to me like the qiagen kit).

You need to check which is good for your experiments like consistency, yield etc. .

We use Invitrogen's maxi kit. But I have used Qiagen's maxi kit in my old lab. I switched to invitrogen because of the time and yield of DNA.

Have you made a LAL assay to proof if the DNA is endotoxin-free?
LAL assays are offered by Cambrex, Charles River and ACC.
If you have still an endotoxin contamination you can removed it using EndoTrap blue (www.endotrap.de)