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

Introduction

In order for DNA to become the information storage medium that serves as an alternative to existing digital storage solution technologies, information must be stored stably in it with the means to repeatedly access and manipulate parts of the stored data.

Current Limitations

Only a few in vitro approaches are capable of addressing some of these requirements, while in vivo approaches still produce largely static data storage libraries. This limitation restricts the real-life applicability of these technologies.

Proposed Solution

In this proposal, we present a new, regeneratable solid-state storage system consisting of beads. In this system, information encoded in single-stranded DNA strands can be:

• Added
• Selectively accessed
• Removed

These operations utilize enzymes and nucleic acid strands as inputs for the different data operations in isothermal reactions with no loss of material.

Strand Architecture

To achieve this, a strand architecture is proposed where unique Data ID sequences are used on the targeted data strands. This allows for performing the intended data operations via enzymatic reactions, including:

1. Addition of data
2. Deletion of data
3. Transcription-based data access

RNA Variant

Furthermore, a variant of this system is proposed that uses RNA molecules for the selective access of the data strands. We aim to implement this in a bacterial data storage system, where RNA-encoding bacteriophages will be used as a non-invasive way to introduce inputs for the data operations, such as:

• Random data access
• Removal of data

Long-term Stability

Finally, we present the use of damage suppressor proteins from extremotolerant organisms. These proteins will complement the in vitro and in vivo system to provide the long-term stability of DNA observed in resilient biological systems.