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Abstract Molecular circuits implemented using molecular components tethered to a DNA tile nanostructure have certain advantages over solution-phase circuits. Tethering components in close proximity increases the speed of reactions by reducing diffusion and improves scalability by enabling reuse of identical DNA sequences at different locations in the circuit. These systems show great potential for practical applications including delivery of diagnostic and therapeutic molecular circuits to cells. When modeling such systems, molecular geometry plays an important role in determining whether the two species interact and at what rate. In this paper, we present an automated method for estimating reaction rates in tethered molecular circuits that takes the geometry of the tethered species into account. We probabilistically generate samples of structure distributions based on simple biophysical models and use these to estimate important parameters for kinetic models. This work provides a basis for subsequent enhanced modeling and design tools for localized molecular circuits.
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Geometric Enumeration of Localized DNA Strand Displacement Reaction Networks
Localized molecular devices are a powerful tool for engineering complex information-processing circuits and molecular robots. Their practical advantages include speed and scalability of interactions between components tethered near to each other on an underlying nanostructure, and the ability to restrict interactions between more distant components. The latter is a critical feature that must be factored into computational tools for the design and simulation of localized molecular devices: unlike in solution-phase systems, the geometries of molecular interactions must be accounted for when attempting to determine the network of possible reactions in a tethered molecular system. This work aims to address that challenge by integrating, for the first time, automated approaches to analysis of molecular geometry with reaction enumeration algorithms for DNA strand displacement reaction networks that can be applied to tethered molecular systems. By adapting a simple approach to solving the biophysical constraints inherent in molecular interactions to be applicable to tethered systems, we produce a localized reaction enumeration system that enhances previous approaches to reaction enumeration in tethered system by not requiring users to explicitly specify the subsets of components that are capable of interacting. This greatly simplifies the user’s task and could also be used as the basis of future systems for automated placement or routing of signal-transmission and logical processing in molecular devices. We apply this system to several published example systems from the literature, including both tethered molecular logic systems and molecular robots.
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- PAR ID:
- 10542531
- Editor(s):
- Seki, Shinnosuke; Stewart, Jaimie Marie
- Publisher / Repository:
- Schloss Dagstuhl – Leibniz-Zentrum für Informatik
- Date Published:
- Volume:
- 314
- ISSN:
- 1868-8969
- ISBN:
- 978-3-95977-344-7
- Page Range / eLocation ID:
- 314-314
- Subject(s) / Keyword(s):
- Localized circuits reaction enumeration DNA strand displacement geometry molecular computing Computer systems organization → Molecular computing
- Format(s):
- Medium: X Size: 24 pages; 2886711 bytes Other: application/pdf
- Size(s):
- 24 pages 2886711 bytes
- Right(s):
- Creative Commons Attribution 4.0 International license; info:eu-repo/semantics/openAccess
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Conference Paper:
- https://doi.org/10.4230/LIPIcs.DNA.30.1
