After doing a PCR, the resulting DNA should be cleaned up to get rid of the primers, polymerases, dNTPs and the various other reagents used in the PCR. This can also be used to remove small fragments of DNA from other sources (such as digestions).

We used Macherey-Nagel's "Nucleospin® Gel and PCR clean-up" kit. The manual can be found here: [http://www.mn-net.com/Portals/8/attachments/Redakteure_Bio/Protocols/DNA%20clean-up/UM_PCRcleanup_Gelex_NSGelPCR.pdf Gel and PCR clean-up Manual]

The kit uses a silica membrane to bind DNA which is then washed with several different buffers. The final step is the removal from the membrane by elution and recovery of our cleaned DNA.

Note: To increase the yield we applied the optional steps in 4 and 5 in the PCR cleanup protocol on pages 18 and 19. By incubating the columns at 70 degrees and eluting the DNA with heated elution buffer the yield of longer fragments can be increased.