Agarose gel for 580bp DNA - What are the suitable conditions? (Jul/18/2006 )

Hi I am trying to extract my PCR gene product of 580bp on agarose gel of about 10 X 8 cm (about 8 wells I think) in 1X TAE buffer...what are the best conditions for it? Currently I am using 1.6% at 100V for about an hour....

Best conditions for extracting from agarose gel - use a gel extraction kit.

Running a 1.6% gel at 100V should b fine as well to c the PCR product.

Do you have a gel purification kit? This would be the most ideal way to purify your fragment from the gel.

Other members may have suggestions for crude, manual purifications.

Eh i think I meant running gel conditions...I have the gel extraction kit...

I think 1.6% is fine but you could go down to 1% or 0.8% and still see it

100V is a bit high for agarose/TAE or TBE...the recommended max to keep the gel from getting too hot, and the bands from warping, is about 5V / cm...so your 8cm gel shouldn't be run more than ~40 or 50V if you want good resolution

in this case i will run my sample in 0.8% agarose gel in 50V for 1 hour

0.8? wouldn't the pores be too big??

this should be ok as the DNA you want to see and further extract is 580bp and quite pure.

0.8% will be fine for 580bp

I would go up to 1% at ~400bp and smaller fragments; I use use 0.8% for anything bigger

but that is just my preference?