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Programmable chemical controllers made from DNA

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Posted November 14, 2013

DNA and RNA molecules are the basis for all chemical regulation inside our bodies and all the living organisms on Earth. Genes, which form our DNA and regulate thousands of biochemical processes taking place inside our bodies, are tiny fragments constructed of nucleic acids sequences. Such system is surprisingly versatile, resilient and microscopic, despite some errors resulting in genetic disorders. Considering these traits, it is a good idea to use the double-helix DNA structure – or at least its fragments – to regulate even more simple biochemical events.

Diagram illustrating the DNA gate production. Credit: nature.com

Diagram illustrating the DNA gate production. Credit: nature.com

This particular idea was the basis of research conducted by the scientists from the University of Washington, California Institute of Technology, University of California and Microsoft Research. The team decided to engineer a prototype molecular structure, which may be used to control chemical processes in a “digital” way. Results of this work were published in a scientific paper in Nature Nanotechnology.

The scientists report a DNA-based nanotechnology, which theoretically could be used to implement the computational core of such programmable chemical controllers. The authors used formal descriptions of chemical reactions and their networks serving as a ‘programming language’ to achieve the goal. This is a direct analogy to our usual computational programming languages except that it is implemented using entirely biochemistry-based tools and measures.

The team notes that it is possible to produce highly pure DNA gates by adapting genetic engineering techniques. The nature of those gates is relatively simple and they could be used as versatile control elements making an alternative to the otherwise ‘complex’ DNA. The sequences of such gates may be produced as components of chemical nanocontroller or could be also used to implement standardized signalling protocol that enables the components of nanocontroller to communicate with each other.

The authors say that it should be possible to engineer customized DNA architectures using formalized chemical reaction networks; these DNA architectures will implement any behavior that can be expressed mathematically. And, unlike the traditional logic circuits, the biochemical nature of developed architecture allows complex signal processing of analogue biological and chemical inputs (signals).

The components of DNA-based controllers may be formed using both biologically and chemically synthesized DNA strands, although the authors indicate that biologically produced DNA reduces number of errors compared to its chemically-derived alternatives.

The researchers implemented several building-block reaction types and then combined them into a network that is capable to execute, at the molecular level, an algorithm, which is used in distributed control systems for achieving consensus between multiple biological agents.

The authors also say, that in the future chemical controllers could be used in such application areas as integrated sensing, computation, actuation, and even smart therapeutics or fabrication methods based on self-organization – in a similar way like it is done in biological organisms, which use complex molecular networks to navigate their environment and regulate their internal state.

By Alius Noreika, Source: Technology.org

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