Small DNA fragment recovery bias with SPRI?

[Squall]

Hi all,

When cleaning up a library (Nextera generated if that is important), how common an observation is it to see bias towards recovery of smaller DNA fragments when using SPRI beads - either Axygen magPCR cleanup OR AMPureXP?

We generate fragments in the range of 150 - 800 for our workflow, but when we clean-up using the beads the distribution skews somewhat to the left towards the smaller fragments (150 - 250).

If this is common, is there a way to minimise the effect? Or can anyone offer me any thoughts on the cause and/or solution?

Many thanks!

[nucacidhunter]

Hi all,

When cleaning up a library (Nextera generated if that is important), how common an observation is it to see bias towards recovery of smaller DNA fragments when using SPRI beads - either Axygen magPCR cleanup OR AMPureXP?

We generate fragments in the range of 150 - 800 for our workflow, but when we clean-up using the beads the distribution skews somewhat to the left towards the smaller fragments (150 - 250).

If this is common, is there a way to minimise the effect? Or can anyone offer me any thoughts on the cause and/or solution?

Many thanks!

It is unusual. Distribution should shift toward larger fragments (average fragment size should increase). Posting electropherograms before and after clean up will be helpful for troubleshooting.