A domain-level DNA strand displacement reaction enumerator allowing arbitrary non-pseudoknotted secondary structures

TL;DR

This paper introduces a novel domain-level DNA strand displacement enumerator capable of modeling arbitrary non-pseudoknotted secondary structures, enhancing the design and analysis of complex molecular systems.

Contribution

It presents a new reaction enumerator that handles diverse secondary structures and mechanisms, with a time-scale separation technique ensuring correctness and avoiding polymerization.

Findings

Handles arbitrary non-pseudoknotted secondary structures

Includes mechanisms like association, dissociation, branch migration, and toehold activation

Implemented in Python and integrated into DyNAMiC Workbench

Abstract

DNA strand displacement systems have proven themselves to be fertile substrates for the design of programmable molecular machinery and circuitry. Domain-level reaction enumerators provide the foundations for molecular programming languages by formalizing DNA strand displacement mechanisms and modeling interactions at the "domain" level - one level of abstraction above models that explicitly describe DNA strand sequences. Unfortunately, the most-developed models currently only treat pseudo-linear DNA structures, while many systems being experimentally and theoretically pursued exploit a much broader range of secondary structure configurations. Here, we describe a new domain-level reaction enumerator that can handle arbitrary non-pseudoknotted secondary structures and reaction mechanisms including association and dissociation, 3-way and 4-way branch migration, and direct as well as remote toehold activation. To avoid polymerization that is inherent when considering general structures, we employ a time-scale separation technique that holds in the limit of low concentrations. This also allows us to "condense" the detailed reactions by eliminating fast transients, with provable guarantees of correctness for the set of reactions and their kinetics. We hope that the new reaction enumerator will be used in new molecular programming languages, compilers, and tools for analysis and verification that treat a wider variety of mechanisms of interest to experimental and theoretical work. We have implemented this enumerator in Python, and it is included in the DyNAMiC Workbench Integrated Development Environment.