Periodic Reporting for period 1 - DURA-store (A dynamic, ultra-stable, random-access RNA retrieval database)
Berichtszeitraum: 2023-10-01 bis 2024-09-30
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.
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.
As part of the DuraStore projects work towards developing a dynamic, in vitro DNA-based storage device a protocol for creating a polystyrene-based solid phase support that allows for the reversible addition and removal of payload sequences has been established.
Additionally, through the development of bioinformatics tools, functional sequence domains of the data encoding DNA strands have been designed and optimized to allow data operations—write, delete, and read— to be performed isothermally at temperatures not
exceeding 37°C with high efficiency and specificity to support a storage system with dynamic capabilities. Moreover, the feasibility of the immobilization and data-encoding strands on SSMD beads and their read out in the solid state data storage device to be performed
has been successfully demonstrated. With these results, the project progresses to test the system with payload sequences encoding data files and evaluate its performance with more complex samples.
In working towards the creation of a universally applicable and easily reversible DNA stabilization strategy, the feasibility of transgenic production and purification of the first set of candidate molecules has been demonstrated with the ongoing work focusing on
optimization to achieve high scale production.
Additionally, through the development of bioinformatics tools, functional sequence domains of the data encoding DNA strands have been designed and optimized to allow data operations—write, delete, and read— to be performed isothermally at temperatures not
exceeding 37°C with high efficiency and specificity to support a storage system with dynamic capabilities. Moreover, the feasibility of the immobilization and data-encoding strands on SSMD beads and their read out in the solid state data storage device to be performed
has been successfully demonstrated. With these results, the project progresses to test the system with payload sequences encoding data files and evaluate its performance with more complex samples.
In working towards the creation of a universally applicable and easily reversible DNA stabilization strategy, the feasibility of transgenic production and purification of the first set of candidate molecules has been demonstrated with the ongoing work focusing on
optimization to achieve high scale production.
The in vitro DNA-based data storage technology that is being developed in the DuraStore project has the potential to move the capabilities of DNA-based data storage towards that of the
digital data storage solution by creating a regeneratable molecular drive that is capable of dynamic data operations, random access without material loss. Through establishing the feasibility
to perform all the required data operations (write, delete, read) with considerably high efficiency and specificity the project is moving successfully towards these goals. Moreover, the system
has the potential to increase the competitiveness of DNA-based data storage technologies by using chemical reactions for carrying out data operations that can be performed at considerably
lower constant temperatures (lower or equal to 37°C) than what existing technologies use and thus offers a strategy for dynamic data storage in DNA with potentially two orders of magnitudes
less energy consumption. However, in order to realize these advantages more experimental work is needed to assess and optimize the performance of the system with more complex data encoding
DNA libraries.
The DNA stabilizing agents the project is developing have the potential to become new form of biological preservatives for DNA, that can be used for stabilizing genetic material in medical,
environmental samples in addition to the synthetic DNA used for data storage in a more easily reversible way compared to existing approaches allowing a more seamless transition to downstream
processes performed on the DNA, while still providing a comparable degree of protection. The confirmation of the feasibility of transgenic production of the molecules is a promising step towards
this goal, nevertheless more experimental work is required to optimize their high scale production.
digital data storage solution by creating a regeneratable molecular drive that is capable of dynamic data operations, random access without material loss. Through establishing the feasibility
to perform all the required data operations (write, delete, read) with considerably high efficiency and specificity the project is moving successfully towards these goals. Moreover, the system
has the potential to increase the competitiveness of DNA-based data storage technologies by using chemical reactions for carrying out data operations that can be performed at considerably
lower constant temperatures (lower or equal to 37°C) than what existing technologies use and thus offers a strategy for dynamic data storage in DNA with potentially two orders of magnitudes
less energy consumption. However, in order to realize these advantages more experimental work is needed to assess and optimize the performance of the system with more complex data encoding
DNA libraries.
The DNA stabilizing agents the project is developing have the potential to become new form of biological preservatives for DNA, that can be used for stabilizing genetic material in medical,
environmental samples in addition to the synthetic DNA used for data storage in a more easily reversible way compared to existing approaches allowing a more seamless transition to downstream
processes performed on the DNA, while still providing a comparable degree of protection. The confirmation of the feasibility of transgenic production of the molecules is a promising step towards
this goal, nevertheless more experimental work is required to optimize their high scale production.