A Modelling and Simulation Tool for DNA Strand Displacement Systems

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Journal Title
Journal ISSN
Volume Title
Perustieteiden korkeakoulu | Master's thesis
Date
2020-06-16
Department
Major/Subject
Security and Cloud Computing
Mcode
SCI3084
Degree programme
Master’s Programme in Security and Cloud Computing (SECCLO)
Language
en
Pages
63+7
Series
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
Supervisor
Orponen, Pekka
Thesis advisor
Gautam, Vinay
Keywords
DNA nanotechnology, DNA strand displacement, rule-based modelling, DSD modelling and simulation, PySB, BioNetGen
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