gel extraction kit will give better result in my opinion. in case of ethanol precipitation, if the ethanol is not properly remove it hinders the ligation reaction. I am not sure what you mean by "size segment sediment in ethanol precipitation procedure".

I hope this helps.

I agree with Ajit, if you do the digestion from a plasmid its better to make gel extraction method

Gel extraction kit for me is better, although it give low yield of the gene, but the purity is high, its important to be sure to get rid of the ethanol after cleaning, and elution in hot elution buffer would increase the efficiency of extraction.

Good luck

Although there will be lost of digested products, gel extraction is better over ethanol precipitation, because (a) ethanol will also precipitate the other digested DNA fragments (b) incomplete removal of ethanol hinder in ligation. Ethanol ppt is better to used for single band DNA PCR purification.

Shakri Banerjee @I mean what size of fragment precipitate in ethanol ppt?does small fragment( 20bp)precipitate?

If you do it properly phenol chloroform extraction and ethanol precipitation is the best for percentage recover and purity but it is easy to mess up. Clean up columns are very quick and easy and usually good enough.

Gel extraction kits are cleaner, faster and easier! If you do digestion from a plasmid, you have no choice to do gel extraction to purify only the fragment that you want. I like Quiagen.

Phenol-Chloro is cheaper but with my experience, it works well only if you have a lot of DNA.

Good luck!