You have purified 2 DNA fragments, generated by BamH I digestion of recombinant DNA plasmid. One fragment is 400 bp and other is 900bp size. You wish to join them together to create a hybrid.
You mix them together in DNA ligase mixture and Incubate them. After 30 min and after 8 hour, you remove sample and analyze them in AGE. You are surprised to find complex pattern of fragments instead of 1.3 kb recombinant molecule of interest. What will be the reason for so many bands observed in original ligation mixture?