A DNA based molecular logic gate capable of a variety of logical operations

Abstract

In this paper we report on a module in the RTRACS (Reverse-transcription and TRanscription-based Autonomous Computing System) molecular computing system, constructed with DNA, RNA and enzymes. The module is a 2-input logic gate that receives input and produces output in the form of RNA molecules. Each of the two input molecules is chosen from a set of two, and the logic gate produces an output molecule for each of the four possible input combinations. Two output RNA molecules can be produced by this module, one for only one combination of inputs, whilst the remaining three combinations lead to the production of the other output. Since the RNA strands can be arbitrarily assigned logical values, this module is capable performing multiple logical operations, including AND, NAND, OR and NOR, given the appropriate mapping of RNA molecules to logical values. We performed numerical simulations of the logic gate reaction scheme, revealing the details of the kinetics of the production of output molecules and the theoretical input–output characteristics. We experimentally demonstrated the proper functioning of the logic gate and the real time production of output molecules. Furthermore, we demonstrate an implementation of the logic gate in diagnosing single nucleotide polymorphism patterns on samples of human genomic DNA. We believe this versatile logic gate has significant advantages as a basic module of RTRACS due to the wide variety of possible logical operations.

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Acknowledgments

The authors gratefully acknowledge Prof. Katsushi Tokunaga and Dr. Nao Nishida, Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, for their help with the preparation of encoding products from the human genomic DNA samples. This work was partly supported by Grant-in-Aid for Scientific Research on Innovative Areas 23119007 to AS from the Ministry of Education, Culture, Sports, Science, and Technology, Japan.

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Correspondence to Akira Suyama.

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Kan, A., Sakai, Y., Shohda, Ki. et al. A DNA based molecular logic gate capable of a variety of logical operations. Nat Comput 13, 573–581 (2014). https://doi.org/10.1007/s11047-013-9394-5

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Keywords

  • Biomolecular computing
  • DNA computing
  • Logic gate
  • SNP genotyping