Tuesday, November 27, 2012

GATTACA Rises: building structures out of DNA

As the 1940's became the 50's, scientists identified the structure and function of DNA as the basic building block of life. Scientists today are using the fundamental ability of DNA to self-organize to engineer nanostructures from IBM microchips to nano-robots. It's the age of DNA origami and with it comes new possibilities for drug delivery, and nanosenors.

Now, physicists at the Institute of Chemistry and Biology of Membranes and Nano-objects at the National Center for Scientific Research in Pessac, France have developed a computer program that describes how DNA strands selectively fold and weave together to form two- and three-dimensional structures.

Program can identify how DNA strands will selectively bind at certain positions.
Source: J.M. Arbona, et. al. Phys. Rev. E 86, 051912 (2012)

The work, published on November 21, 2012 in the journal Physics Review E, is able to accurately reproduce the mechanical and elastic properties of DNA structures and could help researchers determine stable DNA nanostructures, a hurdle in bringing DNA origami to its full potential.

In 2008, Paul Rothemund, a scientist active in DNA nanotechnology but not involved in the new modeling study, gave a TEDTalk that provides a nice explanation for how computer scientists and experimentalists design and fabricate DNA nanostructures:

The new computer model extends current simulations of DNA nanoengineering by accounting for interactions between DNA base pairs, adenine, thymine, guanine, and cytosine. The interactions between base pairs is fundamental both to the internal structure of DNA and to the structures that can be built out of DNA. Using base pair interactions, the model identifies where DNA strands have stable and unstable points for folding or overlapping, enabling researchers to optimize structural properties of DNA origami.

The computer simulations accurately reproduce structural features in fabricated DNA nanostructures, like inter-strand separation, which can be experimentally verified by atomic force microscopy (AFM) measurements.

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