The sensing of small molecules by carefully designed DNA structures reaches its logical conclusion
At its most fundamental level, computation requires that a number of inputs undergo a sequence of logic operations (AND, OR, NOT, and so on) to generate an output. Although silicon is the conventional hardware on which these processes run, replacing it with organic molecules could lead to new computational methods. Now, Wataru Yoshida and Yohei Yokobayashi from the University of California, Davis in the USA have used DNA aptamers (sequences that bind to small molecules) to build logic gates1.
Aptamers for the molecules adenosine and thrombin were linked through a spacer containing a fluorescent dye. Two shorter DNA strands, each partially complementary to one of the aptamer sequences, bind to the parent strand. Each carries a quenching group that reduces the fluorescence of the dye. If either adenosine or thrombin binds to its respective aptamer on the long strand, the base pairing is disrupted and the corresponding short strand is released. Fluorescence stays low, however, because one quencher remains. Only when both small molecules are present — and both short strands are released — does the fluorescence ‘output’ become significant, representing AND logic based on adenosine and thrombin ‘inputs’.
Moreover, the DNA structures were reconfigured to give OR type logic, where the binding of either small molecule results in an enhanced fluorescence output.
Yoshida, W. & Yokobayashi, Y. Chem. Commun. 10.1039/b613201d (2006).
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Cantrill, S. Twisted logic. Nature Nanotech (2006). https://doi.org/10.1038/nnano.2006.138