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Caltech researchers build largest biochemical circuit out of small synthetic DNA molecules
Date:6/2/2011

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Their new logic gates are made from pieces of either short, single-stranded DNA or partially double-stranded DNA in which single strands stick out like tails from the DNA's double helix. The single-stranded DNA molecules act as input and output signals that interact with the partially double-stranded ones.

"The molecules are just floating around in solution, bumping into each other from time to time," Winfree explains. "Occasionally, an incoming strand with the right DNA sequence will zip itself up to one strand while simultaneously unzipping another, releasing it into solution and allowing it to react with yet another strand." Because the researchers can encode whatever DNA sequence they want, they have full control over this process. "You have this programmable interaction," he says.

Qian and Winfree made several circuits with their approach, but the largestcontaining 74 different DNA moleculescan compute the square root of any number up to 15 (technically speaking, any four-bit binary number) and round down the answer to the nearest integer. The researchers then monitor the concentrations of output molecules during the calculations to determine the answer. The calculation takes about 10 hours, so it won't replace your laptop anytime soon. But the purpose of these circuits isn't to compete with electronics; it's to give scientists logical control over biochemical processes.

Their circuits have several novel features, Qian says. Because reactions are never perfectthe molecules don't always bind properly, for instancethere's inherent noise in the system. This means the molecular signals are never entirely on or off, as would be the case for ideal binary logic. But the new logic gates are able to handle this noise by suppressing and amplifying signalsfor example, boosting a signal that's at 80 percent, or inhibiting one that's at 10 percent, resulting in signals that are either close to 100 percent present or nonexistent.

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Contact: Deborah Williams-Hedges
debwmh@caltech.edu
626-395-3227
California Institute of Technology
Source:Eurekalert  

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