Team:EPF-Lausanne/Protocol/GelExtraction

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== Tips ==
== Tips ==
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* Cut away as much Agar as possible. It will play havoc with the spincolumn's filter
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* Cut away as much Agar as possible. It will play havoc with the spincolumn's filter and reduce the yield.
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  and reduce the yield.
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* Minimize the DNA's exposure to the UV-light. UV will damage DNA and have negative effects on any subsequent reactions (for example, [[Team:EPF-Lausanne/Protocol/Ligation|ligations]] can be 10'000x less effective when DNA has been exposed to too much UV light [http://openwetware.org/wiki/DNA_Ligation]
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* Minimize the DNA's exposure to the UV-light. UV will damage DNA and have negative effects
+
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  on any subsequent reactions (for example, [[Team:EPF-Lausanne/Protocol/Ligation|ligations]]
+
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  can be 10'000x less effective when DNA has been exposed to too much UV light [http://openwetware.org/wiki/DNA_Ligation]
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Revision as of 22:11, 24 September 2012

Protocol: Gel Extraction


A gel extraction is used to select a fragment of DNA of a specific length out of a solution composed of different fragments (ideally the difference in length between the wanted fragment and the closest-sized fragment should be more than 200bp). These fragments are often obtained after a digestion.

Start with a lot of DNA (at least 2 ug of DNA to get reasonable yields), and load a gel with it (if possible, leave an empty lane on both sides to avoid contamination, these bands get quite big). When the gel has finished running, put it on a UV light, and locate the correct band. Cut it out (with a razorblade) and put it in an Eppendorf (consider using a 2ml one). Then apply the instructions in your kit.

We used Macherey-Nagel's "Nucleospin® Gel and PCR clean-up" kit. Its 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]

Tips

  • Cut away as much Agar as possible. It will play havoc with the spincolumn's filter and reduce the yield.
  • Minimize the DNA's exposure to the UV-light. UV will damage DNA and have negative effects on any subsequent reactions (for example, ligations can be 10'000x less effective when DNA has been exposed to too much UV light [http://openwetware.org/wiki/DNA_Ligation]