DNA File System Encoding With Asymmetric Oligo Redundancy
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Solution Overview
Problem
Current DNA-based storage technology is limited by its ability to store only one file at a time, has a small file size capacity, is prone to errors due to lack of redundancy, and is economically unfeasible for large files, requiring expensive DNA sequencing.
Innovation Solution
The proposed solution involves encoding a file system and directory structure into a DNA oligo mix using asymmetric oligo counts for critical parts, incorporating error-correcting codes, and employing base-4 or base-8 encoding with black-listed codes to minimize errors, allowing for efficient storage and retrieval of multiple files with enhanced error correction.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Ease of manufacture
If current DNA-based storage technology stores only one file at a time, then encoding simplicity is maintained, but storage efficiency and practicality deteriorate
Solution Approach 1:
The patent segments the file system into multiple components (directory structure, file metadata, file content) and encodes them separately using different oligo counts. This allows simultaneous encoding of multiple files while maintaining manageable complexity through structured organization of encoded segments.
Solution Approach 2:
The patent creates a universal encoding framework that can handle multiple file types and directory structures simultaneously. The encoding scheme is designed to be multi-functional, accommodating various file formats and organizational structures within a single DNA storage system.
2Manufacturing precision
If uniform encoding is used for all parts of target file, then encoding consistency is maintained, but error propagation risk increases
Solution Approach 1:
The patent applies local quality by assigning different oligo counts to different parts of the file system based on their importance. Critical components like directory structure and file metadata receive higher oligo counts for enhanced protection, while less critical content areas use standard counts. This localized differentiation optimizes both consistency and error resilience.
3Reliability
If increased coverage is used to provide redundancy, then error correction capability is improved, but economic feasibility deteriorates
Solution Approach 1:
The patent changes the parameter of oligo count dynamically based on the importance of each encoded component. Instead of uniform high coverage across all data, the system adjusts coverage parameters selectively - applying higher redundancy only where needed for critical file system structures, thereby reducing overall sequencing costs while maintaining error correction capability.
4Measurement precision
If DNA sequencing is performed with high coverage, then error detection accuracy is improved, but cost and complexity increase
Solution Approach 1:
The patent performs preliminary error prevention through asymmetric encoding during the DNA synthesis stage. By incorporating error-correcting codes and asymmetric oligo counts before sequencing, the system reduces the need for high-coverage sequencing to detect errors. This preliminary protective action lowers subsequent sequencing requirements and associated costs.
Data Source
AI summary
Techniques for DNA-based storage of electronic data are described herein. In an example embodiment, a file system is stored in deoxyribonucleic acid (DNA)-based storage. The file system is encoded in a set of DNA oligos, where a DNA synthesizer system synthesizes first DNA oligos that encode metadata of the file system and second DNA oligos that encode the contents of files in the file system.