DNA-encoded REconfigurable and Active Matter

Project Information

DREAM

Grant agreement ID: 101096956

DOI

10.3030/101096956

EC signature date 11 April 2023

Start date 1 September 2023

End date 31 August 2028

Funded under

• European Research Council (ERC)

Total cost

€ 2 496 750,00

EU contribution

€ 2 496 750,00

Coordinated by

ECOLE NORMALE SUPERIEURE
France

Periodic Reporting for period 1 - DREAM (DNA-encoded REconfigurable and Active Matter)

Reporting period: 2023-09-01 to 2026-02-28

Summary of the context and overall objectives of the project

Synthetic soft materials, from emulsions to polymers, have myriad of useful applications. Yet, each material is usually designed for a specific purpose and lacks the versatility and adaptability we can find in living matter. Biological systems, in contrast, can sense their environment, evolve, move and transform in an adaptive manner.
This project aims to bridge this gap by using DNA as a molecular program to give synthetic materials some of these life-like properties. More specifically, the goal is to develop DNA-encoded principles that would allow synthetic soft materials to adapt, evolve, and perform dynamic functions in way similar to what living systems do. To reach this goal, we will develop a new way for DNA molecules to dynamically assemble themselves at room or biological temperature, a process called isothermal and reconfigurable DNA self-assembly. This will enable the construction of miniature structures made out of DNA, such as so-called DNA origamis or nanotubes, which can change their shape or behavior autonomously, or when triggered by external stimuli like light. By attaching proteins to these dynamic and evolutive DNA scaffolds, we plan to design more complex artificial systems that can mimic biological processes. These will include synthetic metabolic pathways that can carry out useful chemical reactions, or programmable catalytic switches that turn specific activities on and off. We will also develop a novel way to discover optimal nanostructures by evolution, allowing useful structures to emerge through iterative self-selection steps. To get more macroscopic properties, the project will integrate gene-containing DNA into materials rich in interfaces, such as liquid films, droplets, emulsions or lab-on-chip systems. This will make it possible to genetically program how these materials will behave. More specifically, using reconstituted cell-free expression systems, the materials themselves will produce interfacially active proteins, which will in turn control their surface tension and dynamic properties. Following this way, we hope to realize new kinds of behavior, such as genetically driven flows, self-propelling droplets, or autonomous sorting systems. By co-expressing functional proteins such as enzymes or antibodies, we plan to ultimately create multifunctional materials that can grow, move, sense, adapt, recognize and/or react, demonstrating in fine the power and versatility of using DNA as a universal code for programming life-like functions in smart synthetic materials.

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

Our project explores how DNA, the molecule of life, can be used as a programmable material to create synthetic systems that grow, adapt, and behave in life-like ways. To do so, our project is organized into three main axes, each advancing a new dimension of DNA-encoded soft matter. The first axis focuses on developing ways for DNA to assemble and reconfigure itself under gentle and physiologically compatible conditions. First, we have shown that DNA nanotubes can grow at room temperature from a few molecular strands, forming long, flexible structures up to 100 micrometers in length. When placed inside cell-mimicking structures, these nanotubes organized into dynamic, cytoskeleton-like networks, demonstrating a high-degree of reconfigurability and adaptability. We also created shape-shifting DNA origamis that can morph between different 2D and 3D shapes. Notably, we have also devised reversible DNA superstructures that can assemble or disassemble under light control. Finally, we have demonstrated for the first time that DNA nanostructures can self-assemble directly in the presence of living cells and brain organoids, paving the way toward programmable nanomachines that can adaptively self-assemble and interact with living systems. These results will constitute the solid ground to develop the second axis of the project devoting to the creation of evolving DNA nanomachines, either to create synthetic metabolic pathways or to discover optimal structures by evolution. The third axis of the project consists in developing the concept of genetically encoded interfaces. Using cell-free protein synthesis, we have already succeeded in producing two kinds of interfacially active proteins: BslA and fungal hydrophobins. This has allowed us to achieve the first genetically encoded control of surface tension, fluid transport and liquid motion in fully synthetic systems.

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)

This research project has achieved a series of major scientific breakthroughs, with five publications and one manuscript under review. Two discoveries, in particular, mark important steps toward creating DNA-encoded reconfigurable and active matter.
1. Ultra-fast DNA self-assembly inside living cells
DNA is not only the support of our genetic code, it can also serve as a building material for nanoscale structures, such as so-called DNA origamis. Traditionally, creating such refined structures requires high temperatures and chemical conditions incompatible with life, meaning they must be fabricated separately and later introduced into cells. In this project, we have developed a gentle, isothermal method allowing DNA origamis to self-assemble in biological media at body temperature (37 °C). Even more remarkably, the process happens in just a few minutes, which constitutes a neat improvement over conventional methods taking over hours to days. Using these new conditions, we have demonstrated for the first time 2D and 3D DNA origamis that self-assemble directly in the presence of living cells and tissues. This breakthrough opens new horizons for building nanomachines that form, adapt, interact and operate in situ with living systems.
2. Genetic control of surface tension and liquid motion
We have also demonstrated that the physical behavior of liquids can be programmed by DNA, not through its self-assembly but a genetic level. Instead of relying on chemical additives to modify surface tension, as it is usually done, we have used a synthetic gene encoding for interfacially active proteins called hydrophobins and expressed them with a cell-free system. The expressed proteins lowered surface tension, allowing us to control fluid behavior through gene activity. By adjusting gene expression, we could fine-tune surface dynamics over time and even generate controllable liquid motion, constituting the first-ever demonstration of genetically encoded liquid transport.