Engineers invent programming language to build synthetic DNA

Sep 30, 2013 by Michelle Ma
An artist's rendering shows DNA structures and a chemical reaction "program" on the screen. A "chemical computer" executes the molecular program. Credit: Yan Liang, L2XY2.com

Similar to using Python or Java to write code for a computer, chemists soon could be able to use a structured set of instructions to "program" how DNA molecules interact in a test tube or cell.

A team led by the University of Washington has developed a for chemistry that it hopes will streamline efforts to design a network that can guide the behavior of chemical-reaction mixtures in the same way that embedded electronic controllers guide cars, robots and other devices. In medicine, such networks could serve as "smart" drug deliverers or disease detectors at the cellular level.

The findings were published online this week (Sept. 29) in Nature Nanotechnology.

Chemists and educators teach and use chemical reaction networks, a century-old language of equations that describes how mixtures of chemicals behave. The UW engineers take this language a step further and use it to write programs that direct the movement of tailor-made .

"We start from an abstract, mathematical description of a chemical system, and then use DNA to build the molecules that realize the desired dynamics," said corresponding author Georg Seelig, a UW assistant professor of electrical engineering and of computer science and engineering. "The vision is that eventually, you can use this technology to build general-purpose tools."

An example of a chemical program. Here, A, B and C are different chemical species. Credit: Yan Liang, L2XY2.com

Currently, when a biologist or chemist makes a certain type of molecular network, the engineering process is complex, cumbersome and hard to repurpose for building other systems. The UW engineers wanted to create a framework that gives scientists more flexibility. Seelig likens this new approach to programming languages that tell a computer what to do.

"I think this is appealing because it allows you to solve more than one problem," Seelig said. "If you want a computer to do something else, you just reprogram it. This project is very similar in that we can tell chemistry what to do."

Humans and other organisms already have complex networks of nano-sized molecules that help to regulate cells and keep the body in check. Scientists now are finding ways to design synthetic systems that behave like biological ones with the hope that synthetic molecules could support the body's natural functions. To that end, a system is needed to create synthetic DNA molecules that vary according to their specific functions.

The new approach isn't ready to be applied in the medical field, but future uses could include using this framework to make molecules that self-assemble within cells and serve as "smart" sensors. These could be embedded in a cell, then programmed to detect abnormalities and respond as needed, perhaps by delivering drugs directly to those cells.

Seelig and colleague Eric Klavins, a UW associate professor of electrical engineering, recently received $2 million from the National Science Foundation as part of a national initiative to boost research in molecular programming. The new language will be used to support that larger initiative, Seelig said.

Explore further: Special microscope captures defects in nanotubes

More information: www.nature.com/nnano/journal/v… /nnano.2013.189.html

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1.3 / 5 (12) Sep 30, 2013
The implications for such a tool, could be considered just below the invention of the electron microscope or the first atomic pile IMHO. As this tool advances, wondrous things can come from it or unbelievable horror...here we go!
word-
flashgordon
1.6 / 5 (13) Sep 30, 2013
We're going into the science future materially, but not spiritually. Will the religious deny us to learn the brain, or any more astronomy? The Hawaians destroyed the potential of the Keck because the baren land up on top of the volcano was 'holy land' according to their delusions!

This is just an example. I remember archaeological digs in Israel that were not allowed because, 'we might figure out the truth.'
Jaeherys
not rated yet Sep 30, 2013
I have been very interested in synthetic biology and DNA programming throughout my academic career, dabbling with in vivo programmed responses to specific morphological changes within the cell. I am involved in the elucidation of the effects of a protein called Nodal on cell migration/invasion and tumor suppressing behaviour. Like most labs, we have to indirectly monitor these effects by common techniques like immunoprecipitation, western blots, quantitative polymerase chain reactions, and immunohistochemistry (fluoresecent tags like green fluorescent protein), etc. These techniques are extremely useful but they all lack conditional responses and realtime, direct analysis.

I may be overestimating the potential of this article as I haven't read the actual publication yet but this is the exact type of framework that is required to thoroughly examine these extremely complex mechanisms with feedback loops, positive and negative regulations, checkpoints, and other enzymatic activities.
alfie_null
4 / 5 (1) Oct 01, 2013
Maybe not an exact parallel, but reading of this made me think of VHDL. Access to inexpensive compilers, coupled with equally inexpensive hardware made the technology accessible to a much broader group of users.
nanotech_republika_pl
1 / 5 (2) Oct 01, 2013
Could this be used, in a future, to store each single neuron ID, the info about its connections to the neighboring neurons and the relevant current state of the connections and the cell itself, and then to activate a fluorescent protein to signal that info to the outside of the brain? All that to allow for mapping the brain to the single cell precision, for a future brain upload. One can imagine some way for slowing down or quieting the brain so such a massive information can be uploaded to an external computer.