Try freeze and squeeze. Run the product on 0.8%agarose (the less agarose the better). Put it in an eppendorf tube and freeze the tube. Freeze and thaw twice is even better. Then spin the tube at top speed for 5 minutes . suck off the supernatant which will be your dna in running buffer
Paul Rutland, Is the supernatant pure with the required size of the fragment, or does it need to be precipitated further? And if it is pure, can such supernatant with dsDNA be used for restriction digestion?
The supernatant will be clean pcr product unless there are 2 bands of the same size and within the limitations of the agarose ( usually can separate bands with a size difference of more than 5%.)
If you want to cut a pcr product then usually you can avoid any loss of product by cutting the pcr product without any purification if your amplification is reasonably clean The database at New England Biolabs shows the expected cutting efficiency in many PCR buffers and is a valuable resource
found here
https://www.neb.com/en-gb/tools-and-resources/usage-guidelines/activity-of-restriction-enzymes-in-pcr-buffers
You can set up a restriction digest by adding the buffer & enzyme directly to your PCR tubes. As long as you have 1 PCR product in the reaction (and you checked the enzyme is compatible with the PCR buffer), then it works great.
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