DNA origami

[J3ny]

Hi,

I was wondering if it is possible to use 3DNA to simulate DNA origami structures (as first presented in Rothemund's Nature paper [2006])? What I am particularly interested in is finding out if given the ssDNA sequences (scaffold and staples) could you predict the final origami shape?

Best wishes and kind regards.

Thanks in advance.

[xiangjun]

Thanks for posting on the 3DNA Forum. I am aware of the beautiful DNA origami. Unfortunately, 3DNA is not directly applicable for predicting the final origami shape given a ssDNA sequence. However, I vaguely remember some publications where 3DNA was used in certain steps of the model building process.

Xiang-Jun

[J3ny]

Thanks for a quick reply.

That's interesting. Do you maybe remember the publications regarding model building process? Or have any hints on how to find them?

I have another question as well: can 3DNA be indirectly applicable for such predictions? What I mean is, given there was a good predictor or simulator for DNA origami which would figure out the topology of ssDNA binding to each other at specific places would it be possible to somehow combine it with 3DNA to figure out the exact geometrics of the structure?

Thanks in advance.

[xiangjun]

One example is by Bai et al. (2012): "Cryo-EM structure of a 3D DNA-origami object", where the authors wrote:

Model Building. An initial atomic model with the designed topology of parallel dsDNA helices in a rectangular lattice and with the known nucleotide sequence was calculated using custom software that relied on 3DNA (23) to calculate canonical B-DNA for all designed helical fragments.

3DNA does not make predictions -- it is simply a toolbox with facilities for manipulations of 3-dimensional nucleic acid structures. It can be applied 'mechanically' in a particularly situation as users see fit. There may be dedicated tools for DNA origami predictions, but 3DNA is not (yet) one of them.

HTH,

Xiang-Jun