I assembled a DNA origami, a 6HB, and I run a scaffold and assembled 6HB in a agarose gel. In a gel, the band of scaffold is higher than 6HB band. actually, the molecular weight of 6HB is more than scaffold, therefore the 6HB band should be higher than scaffold band. But it is not.
Electrophoretic separation in agarose is not just based on molecular weight and charge. The agarose forms a sieve and large structured molecules can become entangled in the pores of the agarose gel particularly if they are irregularly shaped. This is why DNA electrophoresis is generally carried out using denatured DNA. This allows the DNA to form more linear structures, that are less likely to be physically held up by the gel structure.
It s not clear from your coments exactly what type of electrophoresis you are carrying out (other than it is DNA and on agarose of course) and the relative sizes of the scaffold to the origami (though I believe the scaffold is generally many times smaller than the origami which would support this hypothesis) so I am not sure if this advice is relevant to your situation. But you could denature the DNA or move to acrylamide with very large pore size structure (low cross linking) in the hope that both molecules would be freer to move. I hope this helps.
i think the 6hb DNA is folded and has a compact shape while the scaffold is in an extended conformation, therefore scaffold moves laggingly while 6HB moves faster. Just like a supercoiled plasmid runs faster than a linearized plasmid.
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