Bead removal of <1000 bp from LARGE fragments

[cement_head]

Hi,

Trying to prep some very large fragment libraries (>50 kbp), and I've isolated the gDNA using a BluePippin, but when I use beads (Promega ProNex) to clean up, or rather, remove the small fragments (<1000 bp), I get low yield of the input 50 kbp gDNA.

Are there specific beads that are better for this? AMPure XP PB? Suggestions?

Thanks,
Andor

[luc]

The beads are likely all very similar. You could try to elute for a much longer time than usual for short fragments.

[cement_head]

No, I don't want the small fragments. I want only fragments LARGER than 1000 bp.

In essence, I want to eliminate any small (unseen) fragments that may unduly influence a nanopore/ONT minION library prep.

Thanks

[nucacidhunter]

Loss of large fragments mostly can be due to inefficient binding. longer incubation of bead-DNA solution on a rotating wheel should increase recovery.
Quantifying supernatant with PicoGreen or Qubit dsDNA HS assay can point if this is the case.

Circulomics short read eliminator kit is also a good choice.

[luc]

You misunderstood me: Long fragments will require a longer time to elute/dissolve from the beads compared to shorter fragments.

No, I don't want the small fragments. I want only fragments LARGER than 1000 bp.

In essence, I want to eliminate any small (unseen) fragments that may unduly influence a nanopore/ONT minION library prep.

Thanks