Size distribution and library yields will vary depending on the size selection
method. Size selection can be performed using a number of methods including
E-Gel size select gels, standard 2% agarose gels, or AMPure XP Beads (see
protocol below). For E-Gel size select gels, select adaptor ligated DNA in the
190–230 bp range for 100 bp libraries and 290–330 bp range for 200 bp read
lengths. For AMPure XP bead size selection, use the protocol below. Expect
size distributions in the range of 230–270 for 100 bp reads and 310–370 for
200 bp reads.
Table 1: Recommended Conditions for Dual Bead-based Size Selection
*Bead:DNA ratio is calculated based on the original volume of DNA solution.
||INSERT SIZE (bp)
|1st Bead Selection
|2nd Bead Selection
AMPure XP Bead-based Dual Bead Size Selection for 100 bp Inserts
Caution: The following protocol is for size selecting libraries with a 100 bp insert from a 100 µl volume. For libraries with a 200 bp insert please use the bead:DNA ratio listed in the chart above.
1st Bead Selection to Remove Large Fragments:
This step is used to bind the large, unwanted fragments to the beads. The supernatant will contain the desired fragments.
2nd Bead Selection to Remove Small Fragments and to Bind DNA Target:
- Add 90 µl (0.9X) resuspended AMPure XP beads to 100 µl DNA solution. Mix well on a vortex mixer or by pipetting up and down at least 10 times.
- Incubate for 5 minutes at room temperature.
- Place the tube on a magnetic rack to separate the beads from the supernatant. After the solution is clear (about 5 minutes), carefully transfer the supernatant to a new tube (Caution: do not discard the supernatant) Discard beads that contain the large fragments.
This step will bind the desired fragment sizes (contained in the supernatant
from Step 3) to the beads. Unwanted smaller fragment sizes will not bind to the
Note: Be sure not to transfer any beads. Trace amounts of bead carry over
may affect the optimal performance of the polymerase used in the NEBNext
High-Fidelity 2X PCR Master Mix in the subsequent PCR step.
- Add 15 µl (0.15X) resuspended AMPure XP beads to the supernatant, mix well and incubate for 5 minutes at room temperature.
- Put the tube on a magnetic rack to separate beads from supernatant. After the solution is clear (approximately 3 minutes), carefully remove and discard the supernatant. Be careful not to disturb the beads that contain DNA targets (Caution: do not discard beads).
- Add 500 µl of 80% freshly prepared ethanol to the tube while in the magnetic stand. Incubate at room temperature for 30 seconds, and then carefully remove and discard the supernatant.
- Repeat Step 6 once.
- Keeping the tube on the magnetic rack, with the cap open, air dry the beads for 5 minutes.
- Elute DNA target from beads into 45 µl water. Mix well on a vortex mixer or by pipetting up and down, and put the tube in a magnetic rack until the solution is clear, approximately 3 minutes.
- Transfer approximately 40 µl of the supernatant to a clean tube, being careful not to transfer any beads.