Hi
I'm trying to design a simple cube-shaped DNA origami with specific dimensions from just single stranded DNA oligos.
Since there is no specific scaffold the origami is based on, cadnano is difficult to use...
I understand you can use Nupack... but I'm not sure how to create 3d objects using Nupack.
Would there be a better program fit for this or what would be the ways doing so in nupack?
Something like the attached picture?
Nupack won't help you with 3D, I don't think. Check out oxDNA - it's very powerful for small assemblies, but you'll have to be patient. Try and go over the examples first to get an idea of how to use it.
Here's how they simulated a prism in oxDNA http://pubs.acs.org/doi/abs/10.1021/acsnano.5b07664
You could also take a look at vhelix (http://www.vhelix.net/) which is a new DNA nanostructure design programme.
my friend, don't waste the time, CaDNAnoSQ software can do your purpose easly
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