Researchers Create DNA Logic Circuits That Work in Test Tubes

Dec 08, 2006

Computers and liquids are not very compatible, as many a careless coffee-drinking laptop owner has discovered. But a new breakthrough by researchers at the California Institute of Technology could result in future logic circuits that literally work in a test tube--or even in the human body.

In the current issue of the journal Science, a Caltech group led by computer scientist Erik Winfree reports that they have created DNA logic circuits that work in salt water, similar to an intracellular environment. Such circuits could lead to a biochemical microcontroller, of sorts, for biological cells and other complex chemical systems. The lead author of the paper is Georg Seelig, a postdoctoral scholar in Winfree's lab.

"Digital logic and water usually don't mix, but these circuits work in water because they are based on chemistry, not electronics," explains Winfree, an associate professor of computer science and computation and neural systems who is also a recipient of a MacArthur genius grant.

Rather than encoding signals in high and low voltages, the circuits encode signals in high and low concentrations of short DNA molecules. The chemical logic gates that perform the information processing are also DNA molecules, with each gate a carefully folded complex of multiple short DNA strands.

When a gate encounters the right input molecules, it releases its output molecule. This output molecule in turn can help trigger a downstream gate--so the circuit operates like a cascade of dominoes in which each falling domino topples the next one.

However, unlike dominoes and electronic circuits, components of these DNA circuits have no fixed position and cannot be simply connected by a wire. Instead, the chemistry takes place in a well-mixed solution of molecules that bump into each other at random, relying on the specificity of the designed interactions to ensure that only the right signals trigger the right gates.

"We were able to construct gates to perform all the fundamental binary logic operations--AND, OR, and NOT," explains Seelig. "These are the building blocks for constructing arbitrarily complex logic circuits."

As a demonstration, the researchers created a series of circuits, the largest one taking six inputs processed by 12 gates in a cascade five layers deep. While this is not large by the standards of Silicon Valley, Winfree says that it demonstrates several design principles that could be important for scaling up biochemical circuits.

"Biochemical circuits have been built previously, both in test tubes and in cells," Winfree says. "But the novel thing about these circuits is that their function relies solely on the properties of DNA base-pairing. No biological enzymes are necessary for their operation.

"This allows us to use a systematic and modular approach to design their logic circuits, incorporating many of the features of digital electronics," Winfree says.

Other advantages of the approach are signal restoration for the production of correct output even when noise is introduced, and standardization of the chemical-circuit signals by the use of translator gates that can use naturally occurring biological molecules, such as microRNA, as inputs. This suggests that the DNA logic circuits could be used for detecting specific cellular abnormalities, such as a certain type of cancer in a tissue sample, or even in vivo.

"The idea is not to replace electronic computers for solving math problems," Winfree says. "Compared to modern electronic circuits, these are painstakingly slow and exceedingly simple. But they could be useful for the fast-growing discipline of synthetic biology, and could help enable a new generation of technologies for embedding 'intelligence' in chemical systems for biomedical applications and bionanotechnology."

The other authors of the paper are David Soloveichik and Dave Zhang, both Caltech grad students in computation and neural systems.

Source: Caltech

Explore further: Best of Last Week—Confirmed Earth-sized planet, testing twin paradox w/o a spaceship and news we all peak at 24

add to favorites email to friend print save as pdf

Related Stories

Recommended for you

Not just the poor live hand-to-mouth

14 hours ago

When the economy hits the skids, government stimulus checks to the poor sometimes follow. Stimulus programs—such as those in 2001, 2008 and 2009—are designed to boost the economy quickly by getting cash ...

Math modeling handbook now available

17 hours ago

Math comes in handy for answering questions about a variety of topics, from calculating the cost-effectiveness of fuel sources and determining the best regions to build high-speed rail to predicting the spread ...

Archaeologists, tribe clash over Native remains

18 hours ago

Archaeologists and Native Americans are clashing over Indian remains and artifacts that were excavated during a construction project in the San Francisco Bay Area, but then reburied at an undisclosed location.

User comments : 0

More news stories

Male-biased tweeting

Today women take an active part in public life. Without a doubt, they also converse with other women. In fact, they even talk to each other about other things besides men. As banal as it sounds, this is far ...

Not just the poor live hand-to-mouth

When the economy hits the skids, government stimulus checks to the poor sometimes follow. Stimulus programs—such as those in 2001, 2008 and 2009—are designed to boost the economy quickly by getting cash ...

Archaeologists, tribe clash over Native remains

Archaeologists and Native Americans are clashing over Indian remains and artifacts that were excavated during a construction project in the San Francisco Bay Area, but then reburied at an undisclosed location.

Phase transiting to a new quantum universe

(Phys.org) —Recent insight and discovery of a new class of quantum transition opens the way for a whole new subfield of materials physics and quantum technologies.

Imaging turns a corner

(Phys.org) —Scientists have developed a new microscope which enables a dramatically improved view of biological cells.