how does the conformation of DNA molecules affect the migration of them on agarose gel in electrophoresis?

Answer 1

I've answered a similar question in the past

http://answers.yahoo.com/question/index;_ylt=ApDo1VHr18AJSQm6WOxC_8Dsy6IX?qid=20061028024332AAKbYkD

or copy pasting...

"The more bulky the molecule the harder it is for it to move through the gel pores and thus the slower it will run.

The order in a gel would be
circular nicked (so there is no supercoiling)
linear
supercoiled

Obviously from this order supercoiled is the fastest running, though sometimes it can run at the same height as linear.

The migration of linear DNA is the one representative of the actual size."

Answer 2

the smaller molecule migrates faster whereas the larger molecule migrates slower so when the dna is in supercoiled form it is more condensed and its size is reduced so it migrates faster than the other form of dna like circular and open circular form