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Because DNA is soluble in water, is it possible to extract PCR product by dissolving excised gel containing the DNA band of desired length in water, mashing the gel piece with a pestle, centrifuging it and then pipetting out the supernatant ?

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If you mash it with a pestle, you'll likely break the DNA. You can use a low melting point gel and mild heating followed by centrifugation to extract DNA. –  canadianer Aug 13 at 17:57
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why not use this? (qiagen.com/products/catalog/sample-technologies/…) or a similar product? I have used it many many times and it can be done very easily! –  Bez Aug 13 at 19:08
    
@Bez - Well, that would cost around 1-2$ per sample, correct ? –  Anurag Mishra Aug 15 at 14:56
    
@AnuragMishra indeed, however, there might be delivery charges but some times institutes bulk buy and sell it in their own stores and their prices are less and sometimes there are institute based purchase pages which sell the products at the discounted price. ps I'm not promoting any brand or products here and I just put it up as a point of reference. –  Bez Aug 15 at 16:08

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up vote 7 down vote accepted

Yes, this is possible (and I have done it uncounted number of times) - the method is called "Freeze and squeeze". What you basically do is to run the gel, cut out the band of interest (be careful with the UV light, it causes damage to your DNA and also sunburns, so wear appropriate shielding for your face), dissolve it in a buffer, then freeze it in liquid nitrogen (or the -70°C, doesn't matter) and centrifuge it at room temperature for 10 minutes. During this time the ice melts and the agarose pellets at the bottom. Take the supernatant, do a ethanol precipitation (with glycogen when you only have little DNA) and you have nice and clean DNA. No need for expensive kits and is done approximately in 2 hours.

You can find a very nice and detailed protocol here: "Elution of DNA from Agarose Gels" (The rest of the handbook is also very useful).

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Yes, we used to call this method 'freeze-squeeze'. –  Alan Boyd Aug 13 at 18:33
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@Bez: Excitation 290-320 means that it needs to be excited in UV-B (which can cause DNA damage). The only difference is the emission wavelength which is green not orange/red. And that they claim that they are safer than EtBr. –  Chris Aug 13 at 19:31
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PA gels are not dissolving when they are subjected to heat. But we rarely use them. –  Chris Aug 14 at 9:04
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@AnuragMishra No not necessarily. Have a look at this and this article here at stackexchange. They go into detail. In short: Overnight brings no advantage. –  Chris Aug 14 at 11:12
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@AnuragMishra At maximum speed, 14.000 or whatever your benchtop centrifuge can do. –  Chris Aug 15 at 21:50

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