Non-Ideality of a DNA Strand Displacement AND Gate Studied with a Dynamic Bonded DNA Model

TL;DR

This study uses coarse-grained simulations to analyze the non-ideal behaviors of DNA strand displacement AND gates, revealing complex transition paths, kinetic dependencies, and fidelity variations due to transient bubbles and thermal effects.

Contribution

It introduces a dynamic bonding DNA model to investigate non-ideal effects and detailed transition pathways in DNA strand displacement logic gates.

Findings

Transition paths are influenced by transient bubbles and thermal melting.

Gate operation time weakly depends on toehold and domain lengths.

Fidelity varies significantly across different input states.

Abstract

We perform a spatially resolved simulation study of an AND gate based on DNA strand displacement using several lengths of the toehold and the adjacent domains. DNA strands are modelled using a coarse-grained dynamic bonding model {[}C. Svaneborg, Comp. Phys. Comm. 183, 1793 (2012){]}. We observe a complex transition path from the initial state to the final state of the AND gate. This path is strongly influenced by non-ideal effects due to transient bubbles revealing undesired toeholds and thermal melting of whole strands. We have also characterized the bound and unbound kinetics of single strands, and in particular the kinetics of the total AND operation and the three distinct distinct DNA transitions that it is based on. We observe a exponential kinetic dependence on the toehold length of the competitive displacement operation, but that the gate operation time is only weakly dependent on both the toehold and adjacent domain length. Our gate displays excellent logical fidelity in three input states, and quite poor fidelity in the fourth input state. This illustrates how non-ideality can have very selective effects on fidelity. Simulations and detailed analysis such as those presented here provide molecular insights into strand displacement computation, that can be also be expected in chemical implementations.