What can cause under-fragmentation of DNA?
Under digestion is caused by either improper fragmentation time—see the CoA or product box for recommended lot-specific fragmentation time for the supported insert sizes; incomplete mixing of the master mix before or when combined with the sample; or when there is additional EDTA in your DNA sample storage buffer.
For ideal fragmentation, make sure your DNA is stored or eluted in a buffered solution containing Low EDTA TE (0.1 mM), as provided in the xGen DNA Library Prep Kit EZ, to maximize fragmentation efficiency.
If your DNA is in a 1 mM EDTA TE elution buffer used in the final steps of the DNA extraction or purification process, a buffer exchange using a column or bead-based purification step is required.
To avoid a purification step, you can alternatively adjust the amount of Reagent K2 used in the Enzymatic Prep step to no more than 3x to attain the desired fragment length.