Cleanup of Adaptor Ligated DNA - NEBNext Fast DNA Library Prep Set for Ion Torrent (E6270)


  1. Add 180 µl (1.8X volume) of AMPure XP Beads to the sample and mix by pipetting up and down.

  2. Incubate for 5 minutes at room temperature.

  3. Pulse spin the tube and place in a magnetic rack for approximately 2–3 minutes until the beads have collected to the side of the tube and the solution is clear.

  4. Carefully remove and discard the supernatant without disturbing the beads.

  5. Keep the tube on the magnet and add 200 µl freshly prepared 80% ethanol. Incubate at room temperature, for 30 seconds, and carefully remove and discard the supernatant. 

  6. Repeat step 5.

  7. Keeping the tube in the magnetic rack, with the cap open, air dry the beads for 5 minutes at room temperature.
    Caution: Do not overdry the beads. This may result in lower recovery of DNA target.
  8. Remove the tube from the magnet. Resuspend the beads in 25 μl of sterile 0.1X TE (volume may be adjusted for specific gel-based size selection protocol). Incubate for 2 minutes at room temperature.

  9. Pulse-spin the tube and return to the magnet, until the beads have collected to the side of the tube and the solution is clear.

  10. Transfer approximately 20 μl (or desired volume) of the supernatant to a clean tube, being careful not to transfer any beads.

  11. For size selection, select adaptor ligated DNA in the 190–230 bp range for 100 bp read lengths and 290–330 bp range for 200 bp read lengths.