Hi,
Would people who have experience with DNA origami consider this a wise choice? Then obviously buying a scaffold separately? I realised that due to the curved 3D nature of my design there's is no way to check its final folded structure in silico. While I've gone over my design rational a lot its still a lot of pressure.
I'm at the point of ordering for not only my first DNA fabrication but my first experiment in my own right while reading for my PhD.
Hello Simon, you can design your origami using cadnano and checking the final 3D structure with CanDo. Usually the 96 plates are the cheapest way to buy many oligos at once, but that changes from company to company. I didn't get the meaning of the 50bp question, the length of the staples depends on the design you choose.
Thank you gentleman and apologies for my lack of clarity.
I've been using caDNAno but unfortunately my version doesnt show the effects of insertion and deletion events in the simulated model of the helices. (I've checked this by downloading copies of curved structures from the Douglas 2009 paper they too were shown as long straight helices) does your version show curved structures? I'm very jealous. I just want to be sure I have gotten the math right and my structure is actually a ring.
The 50 basepair reference was an unnecessary arbitrary value to just show roughly how long the sequences I'd be ordering in the wells would be. I think I'm safe with what I'm ordering then. I'll buy each of the 71 staples in a 25nm well in a 96 plate by. By my estimates that should be enough to do several foldings.
as I was saying one of the programs that shows you the structures is called CanDo, it will compute the stability of your structure and show you the shape it will have (if it folds properly)
Apologies Alessandro I misread your earlier post! I read 'caDNAno' twice. Thank you I will do that first thing tomorrow. Very helpful!
Hi again Alessandro Ceccarelli. What kinds of structures have you successfully simulated via Cando? I'm finding a lack of correlation between some curved designs characterised via TEM/AFM and their respective deformed shapes in silico.
Well, consider that you adsorb the sample on mica or on a grid using (I guess) positive ions. They can influence the shape of your origami. You can see my last publication for the pictures, but so far I worked on 2D structures, so there are no strange curves in the structure.
Thanks Alessandro. I'm not sure why but I think curved structures arent represented very accurately (Even something simple like a 90 degree curve in a group of connected helices or a gradual curve into a split ring) in simulations. It was nice to have Cando simulations but I think they may have mislead me slightly in my design methodology. Ah well.
Great paper also. Very interesting.
Thanks about the paper.
About CanDo, I don't remeber it very well but I think you have few options to set before the simulation, maybe you should use those to recreate the environment of you sample. Anywa be careful to discard its results too fast, there is always a chance of a stability problem in the design that CADnano couldn't compute, but you can see with CanDo
Good luck with the origami.
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