DSD enumeration

The domain-level representation provides a more coarse-grained perspective on nucleic acid folding than the single-nucleotide-level. At the nucleotide-level every step is a base pair opening or closing reaction and the corresponding rate can be calculated from the free energy change of a reaction. On the domain-level, we consider a more diverse set of reactions in order to compensate for the fine-grained details that can happen on the sequence level. Nuskell uses a domain-level reaction enumeration library [peppercornenumerator], to predict desired and, potentially, undesired reactions emerging from previously compiled signal and fuel species.

The general types of reactions are spontaneous binding and unbinding of domains, 3-way branch migration, 4-way branch migration and remote toehold branch-migration. Peppercorn’s enumeration semantics are justified based on the assumption that the DSD system is operated at sufficiently low concentrations, such that unimolecular reactions always go to completion before the next bimolecular interaction takes place. Under the assumptions of low concentrations, a condensed CRN can be calculated, with reactions that indicate just the eventual results after all unimolecular reactions complete, and with rate constants systematically derived from the detailed reaction network rate constants.

There are many options available to adjust the semantics of reaction enumeration, they are described in detail in [Badelt et al. (2020)].