Two-Domain DNA Strand Displacement

TL;DR

This paper explores the computational capabilities of a specific class of DNA strand displacement structures with nicks, focusing on two-domain single strands and their use in signal-processing gates, emphasizing formalization and verification.

Contribution

It introduces a restricted class of DNA strand displacement systems with structural constraints, enabling formal analysis and mechanical verification of their computational functions.

Findings

Structural restrictions facilitate formalization

Systems are suitable for mechanical verification

Demonstrates potential for reliable DNA-based computation

Abstract

We investigate the computing power of a restricted class of DNA strand displacement structures: those that are made of double strands with nicks (interruptions) in the top strand. To preserve this structural invariant, we impose restrictions on the single strands they interact with: we consider only two-domain single strands consisting of one toehold domain and one recognition domain. We study fork and join signal-processing gates based on these structures, and we show that these systems are amenable to formalization and to mechanical verification.