how will you know mol wt of a DNA sample without running marker...just with help of tracking dye.......

florescence or some other form of chromatography I assume. If you know the sequence you could infer the mol wt. from the concentration.

 

Just speculation though. If you know the sequence you could probably more easily determine the molecular weight, since the masses of base pairs are well known.

Technically you cannot get the correct molecular weight by using markers (at least not electrophoretically). The reason is that the electrophoresis separates by size, however the different bases possess different MWs and such at best you can only estimate the MW based on the DNA size.

 

So my question is, do you really want to know the molecular weight, or the length of the DNA? Of course, both correlate, but the measurement of either may differ.