The first lane is 1kb ladder, the second lane is the ligation reaction, the third lane is plasmid only control. Previously the same PCR product gave clean bands but now it isn't and I don't know why.
Hi Rees Ross
You did not mention which company ladder you are using. The DNA ladder sizes vary from company to company. I cannot guess the size of the ligated product. Anyway, did you inactivate the ligase after ligation? For example, ThermoScientific T4 DNA ligase is heat inactivated at 65°C for 10 minutes or at 70 °C for 5 minutes incubation prior to electro-transformation or agarose gel electrophoresis. For chemically competent cells, heat inactivation is not mandatory. As T4 DNA ligase is a DNA binding protein, it may interfere with the migration of DNA in agarose gel electrophoresis.
All the best!
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