Question

If two bands, one expected size and one near the well, appears after performing a restriction digestion and a gel electrophoresis on a plasmid with a single restriction site, what does the band near the well represent? Does it mean that some plasmids were not digested? Or does it mean that some plasmids were ligated together? What would be the result of these two conditions on a gel?

Answer 1

Solution

• I thing due to only one restriction site on plasmid it shoud make only one fragment per plasmid digestion
• So such fragments runs on gel at appropriate location to form band.
• But there may be a chance to auto ligate DNA due to complimentary base pairing between overhangs produced by restriction enzyme.(condition 2)
• Thatswhy all ligated fragmwnts get stuck near wells.
• If plasmid not digested but it can move at same location of digested plasmid fragment due to same length.(condition 1)