When Degradation Appears, This Indicates That Nuclease The Possible Presence Of Nuclease In The Eluted Plasmid. There Are Several Things To Do:
1) Nuclease Cannot Be Completely Washed Off Especially When End+ E. Coli Host Strain Is Used. Use End-Strain If Possible.
2) Wash The Column Twice With WF Buffer.
3) Use TE Buffer For Plasmid Elution As EDTA Can Inhibit Nuclease Activity. Store Eluted DNA At -20˚C When Not Used.