Construction of a protocell capable of in-situ RNA computation

This project aims to understand the living systems with principles of physics by building a cell mimic using RNA nanotechnology.

Start date
1 October 2022
Duration
Standard project duration is 4 years
Application deadline
Funding source
University of Surrey
Funding information

Tuition fee is covered for UK students at the standard UK rate with stipend paid for the standard UKRI rate (£15,609 per year in 2021-22). Funded by the Department of Physics at the University of Surrey.

About

Motivation

Understanding and engineering living cells, a basic unit of life, is one of the biggest goals in biology. However, even modelling of simple cells like E. coli is a challenging task due to its complexity. A simpler synthetic alternative to real cells – protocells – can therefore be built to design systems with cell-like traits. Protocells can provide us with insight on the principles of biology, and could, in the long run, be used in biomedical applications such as drug delivery and biosensing. Among available biomaterials, RNA molecules can be programmed to perform various molecular computing including logic gates and neural networks. Indeed, RNA molecules are an important part of the regulatory network of living cells, with a significant portion of RNAs being non-coding RNAs.

The project

In this project, you will have the exciting opportunity to build a protocell system bearing rationally designed RNA reaction circuits. State-of-the-art in-situ RNA circuits based on our recent work (Bae et al., 2021, Nano Lett.) will be used to build RNA reaction circuits inside protocells that mimic genetic networks of living cells. Specifically, you will encapsulate RNA transcription machinery consisting of T7 RNA polymerase, DNA templates and ribonucleotides inside of a giant unilamellar vesicle with ~5 μm diameter. The water-in-oil emulsion method will be used for high-efficiency encapsulation of the transcription machinery. The operation of the RNA circuits will be monitored by an external probe or a light-up RNA aptamer system such as Broccoli. The project also involves a significant amount of computational work as you will be rationally designing the interaction between different RNA species using a set of designing rules to implement circuits for logic gates, signal amplification and sensing of biomolecules.

Related links
Research paper

Training and development opportunity

Through this multidisciplinary project, you will be given an opportunity to build your skills and knowledge on cutting-edge topics in physics and biology including RNA nanotechnology, membrane biophysics, synthetic biology, fluorescence spectroscopy and RNA biology. In addition, you will be provided with training on instruments and software tools such as transmission electron microscopy, spectrophotometer and NUPACK. You can also collaborate with international researchers and present your result at national/international conferences. Finally, you will be supported by the supervision team on building your skills as an independent researcher.

The environment

The University of Surrey is at the heart of the town of Guildford. We have a highly diverse research environment with a good gender and ethical balance. The student will have access to the newly installed transmission electron microscope, microplate reader and biochemistry laboratory space for the project with ample supports from professional research staff.

Eligibility criteria

We are looking for an enthusiastic, self-motivated student to work on this exciting project. The ideal candidate will have experience in wet-lab experiments, good communication skills in English and most importantly, a determined mindset to pursue the research project. We are particularly interested in candidates with previous experience in nucleic acids nanotechnology, membrane biophysics and/or synthetic biology.

Applicants are expected to hold a first or upper-second class degree in a relevant discipline (or equivalent overseas qualification), or a lower second plus a good masters degree (distinction normally required).

English Language requirements 

International applicants may also require an IELTS (English-language test) score of 6.5 or above (or equivalent) with 6.0 in each individual category.

 

How to apply

Please apply through the Physics programme page. The application should be submitted as a single PDF file containing CV, personal statement (one page maximum) and contacts for two references. Please clearly state the studentship title and supervisor on your application.


Application deadline

Contact details

Wooli Bae
E-mail: w.bae@surrey.ac.uk

The project will be supervised by Dr Wooli Bae and Prof. André Gerber at the University of Surrey. Wooli Bae is a lecturer at the Department of Physics with the research area of nucleic acid nanotechnology and synthetic biology. André Gerber is Professor of RNA Biology at the School of Bioscience and Medicine with a research interest in post-transcriptional gene regulation mediated by RNA-binding proteins and non-coding RNAs.

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