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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?

-meganamsu-

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

-mdfenko-

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.

-scolix-

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)

-EndoTrap-