DNA logic gates designed and created

California Institute of Technology researchers successfully combined up to 12 different DNA logic gates in five cascading levels, although the process takes hours, they report in the December 8 Science.

A group of so-called logic gates performs each operation. In the A AND C operation, for example, one gate would consist of strand B intertwined with strand A’, which prefers strand A to strand B. When researchers introduce A into a test tube containing this gate, A’ exchanges B for A, leaving B floating free.

To yield D as an output, researchers would add strand C to the test tube along with a second logic gate that contains strand D intertwined with two other sequences. One of these sequence latches onto B, the other to C, and D then floats free, as intended.

The new system can perform relatively complex sequences of operations because it allows the output strand of one operation, such as D, to serve as the input for another logical operation. “The ability to do sophisticated computations relies on the ability to build [these] networks,” Winfree says. “We’ve opened the door to being able to build quite large and complex systems.” Other approaches to DNA computing, such as a system that plays tic-tac-toe, rely on gates made from DNA- or RNA-based enzymes, which have not yet proven as capable of turning their own outputs into inputs.

A crucial part of combining so many gates is purifying noisy input signals, Winfree says. In electronic circuits a whole range of voltages, say 0 to 0.5 volt, would all represent a single input. To accomplish the same effect his group designed gates that act as thresholds, soaking up stray strands until they reach a preset concentration. Other gates amplified correct but weak signals by producing more of a given strand.

More on Nadrian Seeman DNA arms:
Nadrian Seeman and Baoquan Ding of New York University inserted into gaps specially designed DNA cassettes, each of which contains a flipper that swivels from a fixed point on the cassette. Each flipper can project from the array’s surface in one of two different directions, depending on input strands of DNA that are added to the cassettes.

For now the flippers, about 100 total per array, all swivel identically in unison like windshield wipers, but in principle they could be oriented in other ways and controlled individually by specific input strands, Seeman says.

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