Mapping Temporally Ordered Inputs to Binary Message Outputs with a DNA Temporal Logic Circuit

Abstract

Molecular circuits and devices with temporal signal processing capability are of great significance for the analysis of complex biological processes. Mapping temporal inputs to binary messages is a process of history-dependent signal responses, which can help understand the signal-processing behavior of organisms. Here, we propose a DNA temporal logic circuit based on DNA strand displacement reactions, which can map temporally ordered inputs to corresponding binary message outputs. The presence or absence of the output signal is determined by the type of substrate reaction with the input so that different orders of inputs correspond to different binary outputs. We demonstrate that a circuit can be generalized to more complex temporal logic circuits by increasing or decreasing the number of substrates or inputs. We also show that our circuit had excellent responsiveness to temporally ordered inputs, flexibility, and expansibility in the case of symmetrically encrypted communications. We envision that our scheme can provide some new ideas for future molecular encryption, information processing, and neural networks.

DNA Reaction System That Acquires Classical Conditioning

“…Systems with plastic adaptation have memory and learning capabilities and have been actively studied in the field of DNA computing over the past decade, − as pioneered by Qian et al These studies focus primarily on implementing well-established machine learning algorithms, such as neural networks, on DNA reaction systems (hereafter, DNA circuits), while addressing basic learning at the simulation level . In contrast, an operating principle that can alter the circuit functions depending on the history (stimulus level and timing) of the input stimuli while considering the dynamic properties of DNA circuits has been proposed, , implying further possibilities to extend the capability of biochemical reaction systems. − However, adaption to DNA circuits with memory and learning capabilities by exploiting the dynamic properties of biochemical reactions remains challenging …”

Temporal logic circuits implementation using a dual cross-inhibition mechanism based on DNA strand displacement

“…Furthermore, the expanded multi-node cross-inhibition mechanism can be utilized to realize symmetric encryption systems, wherein different input sequences activate distinct inhibitory nodes that convert the input temporal information into encrypted data according to the arrangement of the inhibitory nodes. 47 Despite the existence of various methods for constructing versatile components of temporal logic circuits, such as the temporal AND gate, there still remains a notable scarcity of such versatile components in temporal logic circuits. The diversity of such versatile components is of utmost importance for the construction of complex temporal circuits.…”

“…Furthermore, the expanded multi-node cross-inhibition mechanism can be utilized to realize symmetric encryption systems, wherein different input sequences activate distinct inhibitory nodes that convert the input temporal information into encrypted data according to the arrangement of the inhibitory nodes. 47 …”