Synthesis and analysis of biomolecular circuits using DNA strand displacement

• Main Author: Eyriay, Iuliia
• Format: Dissertation
• Language: English
• Published: University of Warwick 2022
• Subjects: QH Natural history; QP Physiology; TA Engineering (General). Civil engineering (General); TP Chemical technology

This PhD thesis aims to present new results in fundamental research on the DNA strand displacement (DSD) based biomolecular circuits. Programming with DNA offers a number of advantages, including high programmability, structure stability and precise control at the molecular level. The range of applications for DSD systems varies greatly, from healthcare to smart materials and to nanotechnology. This thesis presents new results on how the DSD mechanism can be utilised to design circuits for computing nonlinear functions, in particular, an accurate ratio of two signals and a natural logarithm of a signal. Analysis of the ratio circuit establishes the conditions for the system stability and the upper bound on the maximum tolerable time delay. It is exploited how the elementary circuits can be used in combination to form more complex biomolecular systems, drawing on the example of the natural logarithm circuit. The proposed design shows significant benefits in terms of computational accuracy and the range of input values compared to other methods. The development of tools for automated circuit design is crucial to increasing the speed, accuracy and reliability of the process, allowing to obtain an accurate model of a system almost effortlessly. Despite obvious benefits, nucleic acid circuits are often prone to unintended reactions called leaks, which can significantly compromise circuit behaviour. A new semantics for automated generation of leak reactions in DSD circuits are presented. The semantics can automatically generate complex leak pathways that were previously manually derived while enumerating additional leak pathways. It is also used to improve well-established hypotheses by proposing more leak-resistant elementary circuits. The proposed method could have a potential advantage for testing and developing leak-mitigating techniques. The compiler for translating a transfer function into its DSD implementation is developed to aid the automated design further. In some cases, leak reactions can be used intentionally, for instance, to ensure a slow and constant signal production in a timer circuit. The benefits and challenges of the deliberate use of leaks are investigated by suggesting an alternative timer circuit design that relies on toehold-mediated strand displacement. The proposed design generates fewer leak reactions, and its performance is much less affected by them. When designing synthetic circuits, it is vital to consider how biological and experimental uncertainty affect overall functionality and reliability. The robustness properties of the two timers, subject to parametric uncertainties in the reaction rates, are analysed. The simulation results show that the proposed toehold-mediated timer is generally more robust against investigated uncertainties and particularly robust to uncertainties in the leak rate. As these results show, the suggested circuit has the potential to be practically implementable in future applications.