Programmable Molecular Signal Transmission Architecture and Reactant Regeneration Strategy Driven by EXO λ for DNA Circuits

Abstract

The characteristics of DNA hybridization enable molecular computing through strand displacement reactions, facilitating the construction of complex DNA circuits, which is an important way to realize information interaction and processing at a molecular level. However, signal attenuation in the cascade and shunt process hinders the reliability of the calculation results and further expansion of the DNA circuit scale. Here, we demonstrate a novel programmable exonuclease-assisted signal transmission architecture, where DNA strand with toehold employed to inhibit the hydrolysis process of EXO λ is applied in DNA circuits. We construct a series circuit with variable resistance and a parallel circuit with constant current source, ensuring excellent orthogonal properties between input and output sequences while maintaining low leakage (<5%) during the reaction. Additionally, a simple and flexible exonuclease-driven reactant regeneration (EDRR) strategy is proposed and applied to construct parallel circuits with constant voltage sources that could amplify the output signal without extra DNA fuel strands or energy. Furthermore, we demonstrate the effectiveness of the EDRR strategy in reducing signal attenuation during cascade and shunt processes by constructing a four-node DNA circuit. These findings offer a new approach to enhance the reliability of molecular computing systems and expand the scale of DNA circuits in the future.

Arbitrary Digital DNA Computing: A Programmable Molecular Perceptron Driven by Lambda Exonuclease for Lighting up Concatenated Circuits

“…Because Lambda exonuclease consists of three centrosymmetric subunits with a closed toroidal structure in space, this prevents the enzyme from invading the hidden nick site to hydrolyze the target DNA strand starting with the 5′-phosphate group. Based on the interface reaction mechanism of Lambda exonuclease, we proposed EAST architecture in our previous work . This architecture can connect two sequences with orthogonal relationships (input sequence and output sequence), which inspired us to construct the ReLU activation function in the perceptron, as shown in Figure b.…”

“…This introduces limitations in the circuit design process with restricted decision margins, making it more challenging to obtain credible and stable outputs in practical applications. Biological enzymes give us more flexible approaches to dealing with the information carried by DNA molecules, such as utilizing DNA polymerases, restriction endonucleases, and nicking enzyme (PEN tools) to accomplish cut and paste operations on DNA. − Furthermore, these enzymes exhibit significant controllability in terms of molecular dynamics, making them a primary driver of the development of DNA circuits. ,, …”

A signal transmission strategy driven by gap-regulated exonuclease hydrolysis for hierarchical molecular networks

“…The Point module corresponds to an individual vertex in the undirected graph and is used to screen all the vertices that need to be output in the final clique. The Point module incorporates a previously proposed strategy in our work, which exhibits excellent leakage resistance and ensures the orthogonality of the input and output signals 43 . In Point1 of vertex 1 shown in Fig.…”