I would say so, do you know the hydrodynamic radius of your DNA origami? 

Although SEC separation is influenced by the molecular weight of an analyte, two molecues of the same MW can have differing hydrodynamic radii, which then results in differences in elution time/volume.

If you don't have the hydrodynamic radius of your molecule, MW of DNA = #DNA bp *650 daltons per bp = 4712 kDa (https://www.neb.com/tools-and-resources/usage-guidelines/nucleic-acid-data).

So you could go for an Acclaim SEC-1000 column. This has an MW range of 1000 to 1,000, 000 Daltons. What HPLC setup do you have?

Dear Simon,

I suggest you to go through the following paper by Castro et al., published in Nature Methods, 2011. They have used the same M13 DNA as scaffold, and have resolved different nanostructures in 2% agarose gels. They considered the fastest moving bands as correctly folded ones. Its a very detailed paper.  I am sure you can get a lot of your answers.

Carlos Ernesto Castro, Fabian Kilchherr, Do-Nyun Kim, Enrique Lin Shiao, Tobias Wauer, Philipp Wortmann, Mark Bathe & Hendrik Dietz. A primer to scaffolded DNA origami. Nature Methods8,221–229(2011)doi:10.1038/nmeth.1570

(http://www.nature.com/nmeth/journal/v8/n3/full/nmeth.1570.html?style=0)

best of luck.

SD

Thanks. Those are both very helpful answers. Im currently looking at seperating any salts, or remaining staples, from an origami solution in a passive manner. Im looking to use a filter of correct MWCO size sat on purified water and just leave the solution to filter for an hour or so.

Im trying to avoid using columns. I think they can break origami structures. Im currently eluting directly from gel into a sucrose well cut in the agarose. Another option would be to recover directly from annealing reaction product.

Im looking to get purified structures in purified water in a high yield to recover afm images. For fragile or hard to fold structures this is very beneficial