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Title: A domain-level DNA strand displacement reaction enumerator allowing arbitrary non-pseudoknotted secondary structures
Information technologies enable programmers and engineers to design and synthesize systems of startling complexity that nonetheless behave as intended. This mastery of complexity is made possible by a hierarchy of formal abstractions that span from high-level programming languages down to low-level implementation specifications, with rigorous connections between the levels. DNA nanotechnology presents us with a new molecular information technology whose potential has not yet been fully unlocked in this way. Developing an effective hierarchy of abstractions may be critical for increasing the complexity of programmable DNA systems. Here, we build on prior practice to provide a new formalization of ‘domain-level’ representations of DNA strand displacement systems that has a natural connection to nucleic acid biophysics while still being suitable for formal analysis. Enumeration of unimolecular and bimolecular reactions provides a semantics for programmable molecular interactions, with kinetics given by an approximate biophysical model. Reaction condensation provides a tractable simplification of the detailed reactions that respects overall kinetic properties. The applicability and accuracy of the model is evaluated across a wide range of engineered DNA strand displacement systems. Thus, our work can serve as an interface between lower-level DNA models that operate at the nucleotide sequence level, and high-level chemical reaction network models that operate at the level of interactions between abstract species.  more » « less
Award ID(s):
0832824 1643606 1317694 1213127
NSF-PAR ID:
10182434
Author(s) / Creator(s):
; ; ; ; ;
Date Published:
Journal Name:
Journal of The Royal Society Interface
Volume:
17
Issue:
167
ISSN:
1742-5689
Page Range / eLocation ID:
20190866
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
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