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New software aids design of 3-D DNA structures

Recent demonstrations of the ability to build complex 3-D shapes from DNA (this post and previous work by William Shih and collaborators published in Science August 2009 abstract) create demand for an easier way to design complex shapes from folded DNA strands. Now new software facilitates designing three dimensional shapes using scaffolded DNA origami. Physorg.com points to this written by Anne Trafton, MIT News Office “Origami: Not just for paper anymore“:

… A major hurdle to [designing complex curved and bent structures from a folded DNA strand] has been automation of the design process. Now a team at MIT, led by biological engineer Mark Bathe, has developed software that makes it easier to predict the three-dimensional shape that will result from a given DNA template. While the software doesn’t fully automate the design process, it makes it considerably easier for designers to create complex 3-D structures, controlling their flexibility and potentially their folding stability.

“We ultimately seek a design tool where you can start with a picture of the complex three-dimensional shape of interest, and the algorithm searches for optimal sequence combinations,” says Bathe, the Samuel A. Goldblith Assistant Professor of Applied Biology. “In order to make this technology for nanoassembly available to the broader community — including biologists, chemists, and materials scientists without expertise in the DNA origami technique — the computational tool needs to be fully automated, with a minimum of human input or intervention.”

Bathe and his colleagues described their new software in the Feb. 25 issue of Nature Methods. In that paper [abstract], they also provide a primer on creating DNA origami with collaborator Hendrik Dietz at the Technische Universitaet Muenchen. “One bottleneck for making the technology more broadly useful is that only a small group of specialized researchers are trained in scaffolded DNA origami design,” Bathe says.

… “DNA is in many ways better suited to self-assembly than proteins, whose physical properties are both difficult to control and sensitive to their environment,” Bathe says.

Bathe’s new software program interfaces with a software program from Shih’s lab called caDNAno, which allows users to manually create scaffolded DNA origami from a two-dimensional layout. The new program, dubbed CanDo, takes caDNAno’s 2-D blueprint and predicts the ultimate 3-D shape of the design. This resulting shape is often unintuitive, Bathe says, because DNA is a flexible object that twists, bends and stretches as it folds to form a complex 3-D shape.

A PDF of the paper has been made available by the Dietz Lab at TU Munich here. An accompanying editorial “Into the fold” [abstract, full text requires free registration] gives a one-page overview of DNA origami and its potential applications. It points to the above paper and a paper [abstract] from Shih and his colleagues on purifying DNA nanostructures with improved yield of intact structures, and it discusses what is yet needed for DNA origami to reach its full potential: other and longer DNA single strands to use as scaffolds, improved methods to chemically conjugate functional groups to specific DNA sites, and a “top-down design solution” to fully automate design. Now we know what developments to watch for!

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