Microfluidic platforms for the engineering of continuously-operating, synthetic nucleic acid-based systems

Nucleic acid nanotechnology is a versatile platform for engineering molecular networks. By designing oligonucleotide molecules with specific sequences, one can build complex synthetic systems with predictable and programmable reactions. The most versatile networks are based on "strand displacement" reactions, in which base pairing is used to drive the replacement of one or more strands in a multi-stranded "gate complex". The outputs of these displacement reactions can trigger subsequent reactions, allowing the construction of large networks.

Traditionally, the essential gate complexes are produced via a multi-step process that cannot be realised in situ. Individual strands are separately synthesized, annealed to form multi-stranded gates, and these gates are then mixed to create a network that produces a single fixed output. Traditional strand displacement-based networks cannot operate continuously without an external supply of gates produced in this way. This limitation prohibits their application in engineered or synthetic cells, where networks must continuously respond to their environment using components produced in situ and in real time.

We have recently demonstrated in situ production of multi-stranded RNA gate molecules directly from transcription, utilising self-cleaving RNA ribozyme motifs that convert a folded single-stranded RNA transcript into a multi-stranded complex [Bae et al., https://pubs.acs.org/doi/10.1021/acs.nanolett.0c03629]. These constructs have the potential to underlie continuously-operating strand displacement networks; this project aims to explore this potential using microfluidic "cells" that can sustain continuously-operating networks. The result will be a novel engineering platform for nucleic acid nanotechnologists, and also a vital step in the process of incorporating nucleic acid-based circuits into living cells.

The student will start by developing microfluidic platforms that are appropriate to hosting continuously active nucleic acid-based systems, identifying optimal geometries and materials for the challenge. Subsequently, the student will test nucleic acid-based circuits of increasing complexity in the microfluidic chips built. Both stages of the project will involve significant input from computational modelling; the project is therefore highly appropriate for students seeking an interdisciplinary challenge straddling engineering, nanotechnology and biology.

The 2016 UK Roadmap Bio-design for the Bio-economy highlighted the substantial impact that synthetic biology can bring to the UK and global economies by developing: frontier science and technology; establishing a healthy innovation pipeline; a highly skilled workforce and an environment in which innovative science and businesses can thrive. Synthetic biology promises to transform the UK Bio-economy landscape, bringing bio-sustainable and affordable manufacturing routes to all industrial sectors and will ensure society can tackle many contemporary global Grand Challenges including: Sustainable Manufacturing, Environmental Sustainability Energy, Global Healthcare, and Urban Development. Whilst synthetic biology is burgeoning in the UK, we now need to build on the investments made and take a further lead in training next generation scientists to ensure sustained growth of a capable workforce to underpin the science base development and growth in an advanced UK bio-economy.
This training provided by this CDT will give students from diverse backgrounds a unique synthesis of computational, biomolecular and cellular engineering skills, a peer-to-peer and industrial network, and unique entrepreneurial insight. In so doing, it will address key EPSRC priority areas and Bioeconomy strategic priorities including: Next-generation therapeutics; Engineered biomaterials; Renewable alternatives for fuels, chemicals and other small molecules; Reliable, predictable, and scalable bioprocesses; Sustainable future; Lifelong health & wellbeing.
Advances created by our BioDesign Engineering approach will address major societal challenges by delivering new routes for chemical/pharma/materials manufacture through to sustainable energy, whilst providing clean growth and reductions in energy use, greenhouse gas emissions and carbon footprints. Increased industry awareness of bio-options with better civic understanding will drive end-user demand to create market pull for products. The CDT benefits from unrivalled existing academic-industry frameworks at the host institutions, which will provide direct links to industrial partners and a direct pathway to early economic and industrial impact.

This CDT will develop 80-100 next-generation scientists and technologists (via the funded cohort and wider integration of aligned students at the three institutions) as adept scientists and engineers, instilled with technical leadership, who as broadly trained individuals will fill key skills gaps and could be expected to impact internationally through leadership roles in the medium term. Importantly the CDT addresses key skill-gaps identified with industry, which are urgently required to create and support high value jobs that will enable the UK to compete in global markets. Commercialisation and entrepreneurship training will equip the next generation of visionaries and leaders needed to accelerate and support the creation of new innovative companies to exploit these new technologies and opportunities.

The UK government identified Synthetic Biology as one of the "Eight Great Technologies" that could be a key enabler to economic and societal development. This CDT will be at the forefront of research that will accelerate the clean growth agenda and the development of a resilient circular bioeconomy, and will align with key EPSRC prosperity outcomes including a productive, healthy and resilient nation. To foster wider societal impact, the CDT will expect all students to contribute to public outreach and engagement activities including: open days, schools visits, and science festival events: students will participate in an outreach programme, with special focus on widening participation.

This CDT will contribute to the development of industrial strategy through the Synthetic Biology Leadership Council (SBLC), Industrial Biotechnology Leadership Forum (IBLF), and wider Networks in Industrial Biotechnology and Bioenergy and Professional Institutes.