Eluted plasmid appeared degraded after storage for an extended period of time."

When degradation appears, this indicates the possible presence of nuclease in the eluted plasmid. Refer to the following: (1) Nuclease cannot be completely washed off especially when end+ E. coli hoststrain is used. Use end-strain if possible. (2) Wash the column twice with W1 Buffer. (3) Use TE buffer for plasmid elution as EDTA can inhibit nuclease activity. Store eluted DNA at -20ºC when not used.