Removing short DNA molecules with magnetic beads

This protocol will guide you through the process of removing short DNA strands from your solution. The resulting solution will only have DNA molecules that are longer than the defined threshold. Helpful for PCR reaction cleanup or the library size selection.


  • Magnetic rack
  • Pipette set for 1000, 200 and 20 microliter
  • Timer


  • Magnetic beads for DNA purification, 100-1000 bp range
  • Ethanol 80%
  • Water molecular grade, nuclease-free
  • Pipette tips
    • 1000 microliter
    • 200 microliter
    • 20 microliter
  • Empty test tubes of your format (for example, 1.5 mL "Eppendorf" tubes, etc.)


    1. Take the suspension of the magnetic beads for DNA purification from the fridge
    2. Vortex thoroughly until the suspension is homogenous
    3. Bring the magnetic beads suspension to the room temperature
    4. Decide on the DNA molecule size that you want to preserve
    5. From the table below, select the volume ratio of the magnetic beads and the sample volume; add the selected volume to the sample:
 DNA molecule size Beads to sample volume ratio Add this volume of beads (microliters) to the 50 μL sample
100 1.5 x 75
200 1.0 x 50
300 0.8 x 40
400 0.7 x 35
600 0.6 x 30
700 0.5 x 25
1300 0.4 x 20
  1. Vortex the sample
  2. Incubate on bench for 5-15 minutes, so the DNA absorbs on the beads
  3. Place the sample into the magnetic rack
  4. Wait for the solution to clear (30 seconds - 2 minutes)
  5. Pipette the supernatant out while keeping the tubes on the magnetic rack. The supernatant contains the short DNA and the low molecular weight impurities. The desired DNA is absorbed on the beads.
  6. Perform two wash steps while keeping the tubes in the magnetic rack:
    1. Add 250 microliters of 80% ethanol.
    2. Wait for 30 seconds
    3. Discard the supernatant
    4. Add 250 microliters of 80% ethanol
    5. Wait for 30 seconds
    6. Discard the supernatant
    7. With 20 microliter pipette, remove all the remaining ethanol from the bottom of the tube
  7. Leave test tubes with the beads open for 3-5 minutes on the bench to dry out the ethanol. Don't dry the beads completely, as the DNA yield will decline.
  8. Elute the DNA from the beads:
    1. Remove the tubes from the magnetic rack
    2. Add 20-30 microliter of water or buffer of choice to the tubes with the beads
    3. Vortex the tubes until all the beads are in suspension
    4. Wait for 5-15 minutes on the bench to complete the elution. The desired DNA is now in the solution
  9. Place the test tubes into the magnetic rack
  10. Wait for the solution to clear (30 seconds)
  11. Transfer the supernatant (that contains DNA) to the fresh tubes
  12. Discard the tubes with the beads
  13. Store the rest of the magnetic beads suspension in the +4 degrees C fridge.