agarosegel question - (Mar/29/2006 )

Hi guys,
i have learned that when i want to seperate 2 bands which are 3.1 and 3.7 kb, i have to make a high % gel.Is that correct? I made a 1.6% and 1.8% gel.Let it run many hours. The separation was still not good.
My superviser said now that it was not correct, and I should make a really low % gel to get the bands better separated.
Is that true?
Would be nice to know what is correct.
Thanks
Tanja

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hello tanJa!


What your supervisor told you the second time is correct!

The bigger the size of your bands the lower should be the % of agarose.

for these kind of bands 3.1 and 3.7 kb I would use a 0.7% agarose gel because they are quite big. If you have really small fragments eg. less than 500bp normally special agarose gels of 3-4% are used!

This is logical if you consider that the smaller the fragments the faster they run and viseversa! So an almost 2% gel that you used for such big fragments is not appropriate because your fragments cannot "run" in such a concentrated gel so they cannot be separated!

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