AMPure XP beads are used to quickly clean PCR reactions and are also used in WGS library prep. You can also use them to do DNA size selections! They work well, but are very expensive. I found step-by-step instructions on how to make a home-made version online, purchased the reagents and tried the protocol. I tested the beads by attempting to clean up DNA ladder and I found that the home-made beads work identically to the AMPure XP beads.
Attached is the protocol for making the beads. I followed the protocol exactly. One note, I weighed the PEG-8000 in the fume hood because the fine powder is an irritant if inhaled. I also have attached a picture of my gel comparing clean-up of 100 bp DNA ladder with commercial AMPure XP beads and the home-made substitute.
The picture looks like you just cleaned without size selection. Kristin, have you tried doing a size selection with the home made beads?
In the picture, I cleaned up the ladder using 1.8x bead buffer : ladder buffer to simulate full size range clean up. I haven’t tested a size selection yet, I will post when I do.
I have completed testing of the home-made beads. I have found that they perform exactly the same or possibly better than the commercial version. Robin, a tech in the Aitken Lab, prepared WGS libraries using the homemade beads and they turned out very well.
I am currently using boatloads of these beads, so I plan to test each batch of 60 mL that I make by attempting to clean up ladder using 1.8x beads to retain all fragments, and by attempting a size selection between 300 to 400 bp using my protocol from BioO.
I am really happy with this step-by-step guide that I found. Things are working out well.