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A Specialized Tri-species Comparator for the DNA PEN Toolbox

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Abstract

We introduce a specialized module for molecular programming systems, designed to accelerate the comparison of species concentrations. Like in electronics, co-processors are important to increase the speed of crucial tasks. Concentration comparison is a central operation in DNA computing, similar to variable comparison in its electronic equivalent. This work represents the first attempt to make multiple comparison in a single step, while keeping the mechanism as optimized as possible with respect to enzymatic load.

We first demonstrate a possible implementation of the system, showing that there is no theoretical barrier to the design. In particular, it allows enough freedom in the sequence design to work around potential cross-talks in the system.

We then add our co-processor to a specific DNA computing paradigm, the PEN toolbox, and use it to implement an optimized tristable circuit and compare its performance to the standard design approach existing in the literature. Our design shows improved time response and lower impact on the saturation of key enzymes, making it a useful module for designing large systems.

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Authors and Affiliations

  1. Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo, 112-8610, Japan

    Nathanaël Aubert-Kato

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  1. Nathanaël Aubert-Kato
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Correspondence to Nathanaël Aubert-Kato.

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Aubert-Kato, N. A Specialized Tri-species Comparator for the DNA PEN Toolbox. New Gener. Comput. 33, 231–252 (2015). https://doi.org/10.1007/s00354-015-0306-3

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  • DOI: https://doi.org/10.1007/s00354-015-0306-3

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