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Programming Language Created for Synthetic DNA Chemistry

Georg Seelig

Georg Seelig (University of Washington)

Computer scientists and systems biologists at University of Washington, California Institute of Technology, and University of California in San Francisco are developing a coding language to enable the programming of synthetic DNA chemical interactions. A report from the team led by Washington computer scientist Georg Seelig appeared yesterday online in the journal Nature Nanotechnology (paid subscription required).

Seelig and colleagues hope to make it possible to design DNA molecules to behave with programmed  dynamics that affect biological functions, in much the same way that embedded electronics guide mechanical devices or robotics systems. The researchers envision these synthetic biological controllers being built into devices performing intelligent diagnostics or highly-targeted drug delivery.

While the creation of engineered DNA chemistry is possible, the processes needed to create these molecular systems is complex, cumbersome, and time consuming, often because each of these creations is custom-designed work. Seelig’s team is building more general-purpose tools for designing chemical interactions in DNA that can be expressed mathematically, much like a programming language builds instructions for electronic systems.

The journal article describes a proof-of-concept study by the Washington-CalTech-UCSF team that express several individual chemical interactions derived from synthesized DNA and combines them into a network or template that reflects an algorithm for controlling molecular agents. In the article, the researchers devise and insert genomic templates into plasmid DNA molecules, which are then transformed into E. coli cells. A separate routine identifies and selects the clones, then verifies the plasmid sequence.

This early programming work is part of a larger initiative, funded by National Science Foundation to create a more comprehensive computer-science framework of biochemical circuitry. Seelig, with Washington colleague Eric Klavins, received earlier this month a $2 million grant as part of NSF’s Molecular Programming Architectures, Abstractions, Algorithms and Applications project led by CalTech.

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