DNA- and RNA-Based Computing Systems by Katz Evgeny;

Author:Katz, Evgeny; [Katz, Evgeny]
Language: eng
Format: epub
Publisher: John Wiley & Sons, Incorporated
Published: 2020-12-24T22:30:27+00:00

To design DSD analog computations, one first chooses a suitable formal mechanism. As an example, let's consider the bimolecular reaction . Species A, C, and B are encoded with ssDNA strands composed of a species‐specific and a reaction‐specific domain (respectively, colored and black in Figure 10.1a). The reaction is implemented in two steps with two gates and (Figure 10.1b), which are DNA complexes composed of two or more partially hybridized DNA strands bearing reactive toeholds. First, the step is implemented by that is an AND gate that produces intermediate in the presence of both A and C. A second gate takes the released species as an input and produces B.

Autocatalytic reactions of the type can be experimentally implemented by using a gate that takes two different inputs and generates two identical outputs [25]. The leak inherent to any autocatalytic reaction may be efficiently suppressed by adding a thresholding module that suppresses the output that detaches from the gate in the absence of the input. By connecting three of these autocatalytic modules that repressed each other, Srinivas et al. [25] succeeded the tour de force of synthesizing a DSD oscillator in a closed reactor, thus proving for the first time that complex analog networks with feedbacks can be built and kept out of equilibrium with DSD reactions (Figure 10.1c, d).

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