A Modelling and Simulation Tool for DNA Strand Displacement Systems
Date
2020
Authors
Journal Title
Journal ISSN
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Publisher
Tartu Ülikool
Abstract
DNA is the hereditary material in almost all organisms, and the sequence of its monomers
efficiently conveys essential biological information. Although DNA is well known for its
biological functions, the unique material properties of DNA also motivate scientists to
design and manufacture DNA complexes for technological purposes. This research field
is termed DNA nanotechnology, and it aims to construct arbitrary biomolecular structures
using DNA molecules as building blocks.
DNA nanotechnology initially focused on programmable static structures, but it has
further inspired the designs of engineering systems with dynamic properties such as logic
circuits and catalytic systems. This dynamic variant of DNA nanotechnology is enabled
by the DNA strand displacement (DSD) mechanism. The design of a DSD system
involves discreetly designed initial species that can execute expected sequential reactions.
However, such task is hard to be accomplished by hand as the complete reaction network
of a large-scaled DSD system can be intractable.
In this thesis, we study the problem of modelling DSD systems, i.e., enumerating
combinatorially the full space of molecular complexes reachable from the initial species
and transferring the resulting chemical reaction network to a simulation engine. We
present a rule-based modelling pipeline RuleDSD for generating and simulating reaction
networks of DSD systems. RuleDSD is implemented as a software package DSDPy, a
tool that automatically generates a complete reaction network for a described DSD system
and integrates with the PySB framework for further simulations using the BioNetGen
engine. The reaction networks produced by DSDPy show that it is suitable for modelling
various DSD systems from existing literature.
Description
Keywords
DNA Nanotechnology, DNA Strand Displacement, Rule-based Modelling, DSD Modelling and Simulation, PySB, BioNetGen