Ethanol precipitation of small DNA fragments

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This protocol is for a simple ethanol precipitation of small fragments. This protocol was used to (partially) purify a DNA fragment containing a ribosome binding site (~40 bp) during 3A assembly. The fragment was generated via restriction digest and it was used in a ligation reaction. Note that this protocol simply concentrates your sample and removes enough salts/enzymes for ligation to be successful. All DNA fragments from your digest will still be present in your pellet. These residual DNA fragments do not matter for 3A assembly which selects against incorrect ligation products.

Materials

• Absolute Ethanol (100% = 200 proof)
• 95% ethanol
• Tabletop centrifuge
• -80°C freezer

Procedure

1. Add 2 volumes ice cold absolute ethanol to sample.
   Generally the sample is in a 1.5 mL eppendorf tube. I recommend storing the absolute ethanol at -20°C.
2. Incubate 1 hr at -80°C.
   The long incubation time is critical for small fragments.
3. Centrifuge for 30 minutes at 0°C at maximum speed (generally >10000 g at least).
4. Remove supernatant.
5. Wash with 750-1000 μL room-temperature 95% ethanol.
   Another critical step for small fragments under 200 base pairs. Generally washing involves adding the ethanol and inverting several times.
6. Centrifuge for 10 minutes at 4°C at maximum speed (generally >10000 g at least).
7. Let air dry on benchtop.
   I generally let the pellet air dry completely such that it becomes white so that all residual ethanol is eliminated.
8. Resuspend in an appropriate volume of H₂O.
   Many protocols recommend resuspending in 10 mM Tris-HCl or TE. The advantage of TE is that EDTA chelates magnesium ions which makes it more difficult for residual DNases to degrade the DNA. I generally prefer H₂O and don't seem to experience problems of this sort. If you plan to ultimately use electroporation to transform your DNA then resuspending in H₂O has the advantage of keeping the salt content of your ligation reaction down.

Flexibility Notes

• Some parts of the protocol can be modified to suit your needs, and you should still get reasonably good results. Full disclosure, I didn't write this protocol, only this notes section.

• In place of 95% EtOH for the wash, anything down to about 70% is acceptable.

• In place of a -80, a -40 has worked well for me.

• If a cooled centrifuge is unavailable, a normal one will usually also work (obviously with inferior results, but in my experience, even small fragments reclaimed this way have ligated well)