Isolation of DNA from Agarose Gels (Paper Slurry Method)

This procedure isolates DNA from agarose gels by filtration through a filter-paper column. The column is made in a 500 µL tube from a slurry of filter paper in TE buffer.

 

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Materials

• Whatman 3MM filter paper: 50 cm2 piece
• TE Buffer (10X) : dissolve 186 mg EDTA and 605 mg Tris in 50 mL dH2O; pH to 8.0 with HCl. Store at 4°C, dilute ten times before using.
• Paper Slurry : cut 50 cm2 of filter paper into tiny (1-2 mm2) pieces; add to 40 mL of TE buffer in a 50 mL tube. Shake vigorously by hand for at least 5 minutes. Store at 4°C.
• Agarose gel with DNA to be isolated
• Clean razor blade
• Filter column : Punch a small hole in the bottom of a 500 µL tube with a 23 gauge needle. Remove paper slurry piecewise with tweezers and place over the hole in the 500 µL tube. Pack with a 200 µL pipet tip and remove excess liquid. Repeat until paper column is approximately 3 mm high. Place inside a 1.5 mL tube to collect eluent.

 

Procedure

1. Excise the DNA band from the surrounding gel with a clean razor blade; be sure to remove as little gel as possible.
2. Dice the excised gel fragment into small pieces with the same razor; transfer onto filter column.
3. Centrifuge for 10 minutes at highest speed (approximately 20,000g) in a microcentrifuge.
4. Transfer eluent to a fresh tube; recentrifuge agarose
5. Combine eluent with that from previous centrifugation
6. Assemble a second spin column and transfer remaining agarose to the new column. Spin again.
7. Combine all eluent fractions and concentrate via cold ethanol precipitation