To do that, or course, you need software, so it's great to see that there is already free software that lets you create DNA-based nanostructures:
caDNAno is open-source software based on the Adobe AIR platform for design of three-dimensional DNA origami nanostructures. It was written with the goal of providing a fast and intuitive means to create and modify DNA origami designs. You can learn how to use it, download a copy of the program and some example designs, or even modify the source code.
The software makes heavy use of several fantastic open-source libraries and resources, especially Papervision3D for 3D rendering, Michael Baczynski's AS3 data structures and tutorials, the Tango Desktop Project for icons, and the Blueprint CSS framework for this website. Additional people and resources are acknowledged on the links page.
As you can see from this, there's already quite a rich ecosystem of free code in this area, which augurs well for the future. The last thing we need is for nanotechnology to turn into the smallest black box ever made.
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