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Old 03-03-2015, 09:35 AM   #1
Squall
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Location: Ireland

Join Date: Feb 2015
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Default Small DNA fragment recovery bias with SPRI?

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!
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Old 03-03-2015, 07:54 PM   #2
nucacidhunter
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Location: Melbourne

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Default

Quote:
Originally Posted by Squall View Post
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.
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