MIT researchers’ software ‘can do’ DNA structure prediction
by Amy Swinderman  |  Email the author


CAMBRIDGE, Mass.—Lending a helping hand to researchers who are creating complex DNA designs, a team at the Massachusetts Institute of Technology (MIT) has developed software that helps to automate that process, making it easier to predict the three-dimensional shape that will result from a given DNA template.

The software builds upon the concept of DNA origami, a design strategy pioneered about five years ago by Caltech computational bioengineer Paul Rothemund that enables the construction of two- dimensional shapes from a DNA strand folded over on itself and secured by short "staple" strands. In 2009, Harvard Medical School scientist William Shih extended this concept to the self- assembly of DNA into nanoscale 3D shapes.

Seeking to eliminate the hurdle created by an inability to automate this design process, however, an MIT team led by biological engineer Mark Bathe has developed software that makes it easier to predict how the DNA might twist, bend and stretch as it folds to form a complex 3D shape.

An assistant professor who is starting his third year at MIT, Bathe and his colleagues have been working broadly on "computational physics and biochemistry problems at the molecular and subcellular levels," and are interested in integrating physical models of DNA or cells with data.

In the Feb. 25 online version of Nature Methods, Bathe and his colleagues published a primer on creating DNA origami with collaborator Hendrik Dietz at the Technische Universitaet Muenchen. Called CanDo, the software interfaces with Shih's caDNAno software and predicts the ultimate 3D shape of the design.

While the software doesn't fully automate the design process, Bathe says designers can use it to more easily predict complex 3-D structures, controlling their flexibility and potentially their folding stability. The paper also introduces a computational tool for predicting the structure of DNA origami objects and provides information on the conditions under which DNA origami objects can be expected to maintain their structure.

"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. "The idea behind our software is that there are many ways in which you can connect or join up DNA to make any given shape. Currently, this process is done by hand. Depending on what choices you make, there may be many consequences on an actual folded structure. Moreover, the structure may be flexible on some regions, and stiff in others. We need a predictive, physics-based tool that accounts for the physics of DNA and predicts its shape once it is folded and assembled."

Designers of DNA origami can access this resource at, where they can submit a caDNAno file and receive a computational prediction of single- and multi-layer DNA origami structures, including their mean deformed 3D conformation and conformational flexibility.

Very shortly, Bathe's team will submit a follow-up article detailing how CanDo works and performs in more extensive experimental validation and demonstration. Ultimately, Bathe says the automation of DNA origami may facilitate the creation of "DNA carriers" that can "smuggle," or transport, drugs to specific destinations in the body. For example, in tumors, such a carrier would release its "cargo" based on a specific chemical signal from the target cancer cell.

"The idea is that once you can program structures at a nanoscale level and tether molecules onto a structure, the drug contained within the vessel can bind to a specific set of molecules," Bathe says.

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