DNA Computer Does Math, Plus Lays Out Building Blocks For Bigger Circuits

80beatsBy Valerie RossJun 4, 2011 12:33 AM


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Diagram of the new DNA circuit

What's the News: Researchers have built the most complex DNA-based computer yet, a circuit of 130 strands of DNA that can compute the square root of numbers up to 15. The system, reported

today in Science, is made of biological logic gates, which do computations using DNA strands' natural propensity to zip and unzip. This new method is easily adapted for different calculations and can be automated, meaning it could be used to build much larger circuits. How the Heck:

  • The researchers started with strands of synthetic DNA, some on their own and some paired up. These DNA fragments were designed to take advantage of DNA's ability to zip (fitting together two complimentary strands, like in a double helix) and unzip (pulling the strands apart). When a single strand of DNA found a complimentary sequence to bind to at the tip of a pair of strands, it zipped itself on to one of them, displacing the other strand in the process.

  • The scientists used the double strands as logic gates, the type of device that performs "AND" and "OR" computations in a silicon computer. The single strands of DNA served as inputs and outputs. When a single strand (input) binds to one strand of a pair (gate), it unzips and releases the pair's other strand (output). (There's a helpful diagram of the process here.) That newly single strand can then serve as the input for the next gate.

  • To calculate the square root of a number, the researchers started with four DNA strands representing the binary digits of the number, then mixed them up in a tube with the DNA logic gates. After a series of computations, the circuit spit out the square root by way of fluorescent chemicals, with each color signaling the value (1 or 0) of the binary answer's digits.

What's the Context:

  • Using DNA for computation isn't a new; mathematician Leonard Adleman first published the idea in 1994.

  • But until now, scientists have built each circuit from scratch, a painstaking method that limited the size and flexibility of DNA computation systems. A toolkit of zipping and unzipping DNA strands that can form various combinations will essentially let researchers use a compiler, the same sort of computer program software engineers use to translate their commands from typed-in code to simple instructions silicon circuitry can use, to make these systems. DNA circuit–builders can just say what they want the circuit to do, and a program can find the molecular bits and pieces that can do it.

  • This will enable larger, more sophisticated circuits. One of the researchers calculated that it's possible to make the system 20 times bigger.

Not So Fast:

  • While this DNA-based circuit works on the same principles as silicon circuits, it's quite a bit slower. Getting from initial input to final answer took about 10 hours.

  • This new type of circuit also has other limitations, including the fact that it can't store values in memory.

The Future Holds:

  • Scientists aren't trying to make DNA computers that can compete with silicon ones, particularly given the vast difference in speed.

  • Instead, the advantage of DNA-based computing is that these circuits is that these circuits work in a "wet molecular environment," as Adleman puts it, making them good candidates for doing computation inside cells.

  • More advanced circuits, scientists hope, could be used to diagnose diseases by analyzing chemicals or proteins in a cell, using those molecules as inputs. One researcher is already working on a DNA computation–based test to diagnose malaria.

  • The researchers also hope to speed up the computation by using a support structure to keep the DNA gates close together, rather than letting them diffuse through a test tube.

Reference: Lulu Qian and Erik Winfree. "Scaling Up Digital Circuit Computation with DNA Strand Displacement Cascades." Science, June 3, 2011. DOI:10.1126/science.1200520

Image: Science

, Qian & Winfree

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