chloroform v. phenol/chloroform/isoamylalcohol extraction of plasmid DNA - advantages/ disadvantages of each? (Dec/10/2005 )

I've been reading a few protocols to clean up alkaline lysis preps of plasmid DNA.

Some use chloroform to extract DNA, others use phenol/chlorofom or phonol/chloroform/isoamyl alchohol.

Is there any difference in using each of these three solutions, and which if any is best? I want to make DNA suitable for transfection.

Anyone got any idea (prob a really stupid question!!)

Transfection: Higher purity and yield is needed. Please choose the anion-exchange technology kits or magnetic technology.
Sequencing: both purity and yield need not to be high. please choose the silca technology because this is faster and cheaper.

Many commerical companies these kits such as Qiagen, Invitrogen, DRI

If you are using the plasmid for transfection, the requirement (quality & yield) is higher. I suggest using a commerical kit to get the success easier and faster.

It is sad that processes such as DNA extraction have become like a kitchen recipe, where you dont know what you are putting to your pot. But I agree with Sally in this case, for a better transfection efficiency you need high quality DNA that can be obtained with those kits, nevertheless If you want to keep tryi ng I would use the chloroform protocol which uses less reagents and is easier to evaporate

Me's not too experienced though.. but alkaline lysis also helps get rid of genomic DNA too, I suppose. How would using any of these organic solvents help then? They would only help precipitate Protein out. For that purpose it think.. u can start with 2 or 3 solvents (that's a mix) like phenol/chloroform or phenol/chloroform/isoamylalchohol in equal proportions and then remove them using one solvent like just chloroform, and then remove chloroform (easy evaporation)!

What say, all?

It is advisable to use comercially available columns for your preps if you are using DNA for transfection.