A dynamic, ultra-stable, random-access RNA retrieval database

Project Information

DURA-store

Grant agreement ID: 101115410

DOI

10.3030/101115410

EC signature date 21 April 2023

Start date 1 October 2023

End date 30 September 2028

Funded under

• The European Innovation Council (EIC)

Total cost

€ 1 659 570,00

EU contribution

€ 1 659 570,00

Coordinated by

KAROLINSKA INSTITUTET
Sweden

Periodic Reporting for period 2 - DURA-store (A dynamic, ultra-stable, random-access RNA retrieval database)

Reporting period: 2024-10-01 to 2026-01-31

Summary of the context and overall objectives of the project

Current technologies for long-term data storage struggle to sustainably accommodate the world’s rapidly growing data generation, highlighting the need for new approaches.
DNA is emerging as a promising alternative storage medium as if fully realized, it offers several advantages such as high data density, long-term stability, established production and decoding infrastructure, and low maintenance costs.
However, existing DNA-based data storage technologies mainly support cold-storage applications with limited practical utility.
For DNA data storage to serve as a viable alternative to existing digital storage technologies, fundamental challenges must be overcome to enable the stable but dynamic storage of data in DNA.

The Dura-store project seeks to tackle these challenges through the use of bio-inspired solutions to improve existing DNA data storage technologies in terms of data stability and dynamic data operability in vitro and in vivo, moving the capabilities of these technologies in all aspects towards that of digital data storage and thus improving their commercial competitiveness and adaptability.

The project has three main objectives:
• To create a proof-of-concept solid state data storage device that permits isothermal data-operation reactions utilizing nucleic acid guided enzymatic reactions, which will eliminate the need for temperature cycling and through this increasing the lifetime of the stored material while decreasing the costs of data operations.
• To implement elements of the in vitro system in bacteria to create in vivo data storage solution that is capable of dynamic data operations and random data access by utilization of bacteriophages as input.
• To create a universally applicable and easily reversible strategy for stabilization of DNA for in vitro and in vivo storage systems using biomolecules derived from extremophile organisms.

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

As part of the DuraStore project’s work toward a dynamic, in vitro DNA-based storage device, an improved protocol for a polystyrene-based solid-phase support has been established. This allows for the reversible addition and removal of data payloads with orders of magnitude improvement in efficiency and specificity. The project has also created a new strand design optimized for biochemical data operations—write, delete, and read—on our refined Solid Phase Molecular Drive (SPMD). We demonstrated that all operations can be performed isothermally at temperatures not exceeding 37°C with high efficiency and specificity.

Finally, an improved bioinformatics pipeline was used to encode a data library consisting of 100 binary pixel-art images. We successfully loaded this library onto our SPMD and retrieved the stored information. These results bring the project into its final phase: achieving a fully operational, dynamic molecular data storage drive by validating all data operations on the library loaded onto the SPMD platform.

Furthermore, we have successfully designed and validated the molecular architecture for a targeted 'random access' retrieval system compatible with the in vivo systems to be developed for dynamic data storage in bacteria. Our next steps involve the full integration of this retrieval system with the solid-phase platform to further characterize and optimize it before moving into living systems.

In working toward a universally applicable and easily reversible DNA stabilization strategy, we validated a biological production strategy that resulted in significantly improved yields. We are now scaling this production to meet the project's requirements. In parallel, we successfully confirmed the protective effects of this stabilization strategy against enzymatic cleavage. Our upcoming work will focus on fully characterizing the protective efficacy of this approach against a range of environmental factors, including thermal and chemical stress.

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)

DuraStore transitions DNA-based storage from a static medium to a dynamic, sustainable "molecular drive." While current technologies rely on destructive sampling and energy-intensive thermocycling, DuraStore moves the field closer to the performance of conventional data storage technologies through several key innovations.
Existing DNA storage suffers from material depletion during the "read" process. DuraStore is the only system promising entirely lossless, non-destructive access. Our regeneratable molecular drive enables random access and repetitive operations without the material loss typical of PCR-based retrieval. We have validated this by successfully demonstrating dataset loading and targeted access, confirming the system's ability to handle complex data structures.
We demonstrated that write, read, and delete operations can be performed chemically at ambient temperatures (≤37°C). This eliminates high-temperature steps, offering a strategy with two orders of magnitude less energy consumption than state-of-the-art approaches.
Furthermore, DuraStore is the only DNA-based architecture implementing a scalable targeted delete operation, critical for GDPR compliance. This allows selective removal of data blocks without compromising library integrity, addressing a major barrier to the commercial adoption of biological storage.
Beyond storage, we are developing reversible DNA stabilizing agents providing high-performance protection against heat, radiation, and enzymatic degradation. Unlike silica-encapsulation, our approach ensures a seamless transition to downstream processes, making it ideal for medical or environmental samples. We have validated its enzymatic protection and are currently characterizing its our technologies shielding effects against other factors.

Objectives of the Dura-store project