A DNA NANOtechology toolkit for artificial CELL design

Project Information

NANOCELL

Grant agreement ID: 851667

DOI

10.3030/851667

Project closed

EC signature date 4 October 2019

Start date 1 January 2020

End date 30 September 2025

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 497 477,00

EU contribution

€ 1 497 477,00

Coordinated by

THE CHANCELLOR MASTERS AND SCHOLARS OF THE UNIVERSITY OF CAMBRIDGE
United Kingdom

Periodic Reporting for period 4 - NANOCELL (A DNA NANOtechology toolkit for artificial CELL design)

Reporting period: 2024-04-01 to 2025-09-30

Summary of the context and overall objectives of the project

The astonishingly rich phenomena that we observe in biology emerge from the complex behaviours and functionalities sustained by biological cells. The ability to replicate these responses in completely artificial microrobots, dubbed "artificial cells" is one of the great scientific challenges of our times that, once achieved, could revolutionise our understanding of life, its origin, and importantly have a massive impact on healthcare technologies. For instance, one could think of utilising artificial cells as in-vivo therapeutic agents, capable of sensing the presence of a disease and responding by locally producing and delivering a therapeutic agent, hence enabling personalised therapeutic solutions with reduced toxicity and lower risks compared to approaches based on biological cells.

Artificial cells, are typically constructed from the bottom-up, starting from non-living molecular components that make up their structural elements (e.g. artificial membranes) and give them the ability to respond to stimuli. Most often scientists constructing artificial cells borrow molecular components from biological ones, using them for the same purpose for which they had evolved in the first place. While very powerful, this approach is somewhat limited, as nothing forbids us from including non-biological and non-natural components in artificial cells, which can further expand their range of capabilities and afford overall better control on their responses.

NANOCELL focused on constructing artificial cells almost entirely reliant on non-biological, synthetic DNA nanostructures, utilising the tools developed in the now well-established research field of DNA nanotechnology. This approach sees DNA as a building material, rather than a genetic element, and exploits the selectivity of base-pairing to construct nanoscale objects of very well-defined structure and interactions. In our artificial cells, synthetic DNA nanostructures fulfill both structural and functional roles, roughly equivalent to what proteins do in biological cells.
A central element of the NANOCELL platform are membrane-less organelles self-assembled from DNA nanostructures. These enable the segregation of responsive elements in different environments within each artificial cells, a key pre-requisite for building complex responses.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

The first year of NANOCELL was seriously impacted by COVID, as we experienced extended periods of laboratory closure and restricted access for most of the year. Nonetheless, we managed to make good progress, particularly on the structural aspects of the DNA-based artificial cells. The team deepened our understanding of the DNA-based building blocks that are central to NANOCELL and developed protocols to construct complex cell-like architectures in which DNA-based organelles are enclosed within semi-permeable lipid–DNA membranes.

During the second year of the project, we further consolidated the structural work carried out in year one, accumulating final data that were collated into multiple manuscripts submitted in year three. We also introduced a new concept for sculpting the internal structure of DNA-based synthetic cells, which relies on the design of reaction–diffusion processes to create organelle-like microenvironments within the cells.

Over the following year, we worked to embed new functionalities within the artificial organelles, enabling us to engineer complex behaviours in the artificial cells. These include the ability to respond to a wide range of environmental stimuli, to synthesise, capture and release molecular cargoes, and to trigger the self-assembly of other types of nanostructures that play functional roles within the constructed artificial cells. We also explored a new paradigm for constructing membraneless organelles based on RNA rather than DNA nanostructures. These can be synthesised enzymatically, which unlocks new capabilities for functional responses that place high demands on material and energy input.

In the fourth year of the project, following the relocation of the team from the initial host institution (Imperial College London) to the University of Cambridge, we consolidated work on artificial cell functionalities and succeeded in constructing complex artificial cells in which DNA organelles are enclosed within semi-permeable lipid shells and can sustain complex responses, including the ability to grow and reshape by producing new nucleic acid building blocks. We additionally completed work on RNA organelles and carried out further exploration of the enzymatic production of the organelle-forming nucleic acid nanostructures in living cells (bacteria).

In the final phase of the project (fifth year and nine-month extension), we consolidated work on complex functional artificial cells demonstrating spatial organisation of activities (e.g. enzymatic activity, assembly and disassembly), completed complementary work on morphological engineering of DNA and RNA organelles, and went beyond the initial objectives of the project by testing new materials for the construction of synthetic cell membranes.

These results briefly summarise here have been published in ~30 peer-reviewed papers, and a few more are currently in the pipeline (or available as preprints) and will be published in the coming months.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

NANOCELL has developed a comprehensive, DNA-nanotechnology-based toolkit for the construction of artificial cells.
This toolkit allows us to prescribe complex behaviours such as environmental sensing, communication with biological and artificial cells, information processing, synthesis/capture/release of functional molecular cargoes.

A DNA-based artificial cell. The cyan objects are synthetic organelles made of DNA nanostrucures.