Hi
Hollow DNA spheres. Im not getting a good number to stick to mica for imaging and they seem to be aggregating when I try and get a size distribution of them in a zetasizer.
Im trying to use a MWCO column to purify/concentrate them into purified water which I could then apply directly to a mg treated mica substrate, nitrogen dry, and then hopefully get a good number of spheres in a single image. Obviously if this leads to large clumps of DNA origamis they would not be visible...
I dont know how to solve the zetasizing problem. Are DNA origamis likely to aggregate over time? Id have thought not due to electrostatic repulsion but I could be wrong.
Thanks for your time
First - why do you think they are hollow spheres, all or most? I would expect you have some sequence or sequences that a design program says should be able to form spheres. But if you put your sequences into mfold, you will see all sorts of things unless they are quite small.
If they are small, then you have to do them by hand. Look at how things could link up and figure out ways they can form other patterns.
I haven't handled these, but you might be pulling them apart in your column perhaps. You might be melting them with pH changes. Also, what's the temperature you are working at? DNA's melting point is in a range depending on AT vs GC content. If you melt your spheres, all bets are off.
I would also consider talking to the electron microscopy group about imaging what you have so you can maybe see what's happening. That is, unless you are the EM group. ;-)
Hi Simon,
What buffer do you fold the structures in? Depending on design you should probably fold them in a buffer with ~ 10 mM MgCl2 or in 1x PBS.
If you wash them into only purified water i would expect the structures to degrade quite rapidly. I would recommend you to wash the structures into the same buffer that you folded them in.
Washing the structures in MWCO can sometimes cause the structures to aggregate, could you perform your AFM experiments without first washing the structures?
Cheers
Erik
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