DNA Linker-Symbol Encoding for Higher-Density Data Storage
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Solution Overview
Problem
Existing DNA-based storage schemes require a substantial amount of non-coding linker nucleotide sections, leading to inefficient use of storage volume and the need for a large number of reservoirs to encode data, as they only encode data using nucleotide sequences of symbol sections and not linker sections.
Innovation Solution
Encoding schemes that utilize nucleotide sequences of both symbol and linker sections in DNA strands, reducing the length and volume required for data storage and minimizing the number of reservoirs needed by encoding data in linker sections as well as symbol sections.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Ease of manufacture
If DNA storage uses only symbol sections for data encoding, then the structure is simple and easy to manufacture, but the storage density is low and volume efficiency is poor
Solution Approach 1:
The patent applies universality by making both symbol sections and linker sections serve the dual function of structural connectivity and data encoding. Linker sections, which originally only connected oligos, now also encode data through their nucleotide sequences. This multi-functional design increases storage density without complicating the manufacturing process, as the same synthesis mechanisms are used for both section types.
Solution Approach 2:
The patent transitions from one-dimensional data encoding (symbol sections only) to two-dimensional encoding by utilizing both symbol and linker sections. This dimensional expansion in the encoding space allows significantly more data to be stored in the same physical DNA volume, effectively doubling or tripling the storage capacity without increasing physical size.
2Device complexity
If DNA storage uses only symbol sections for data encoding, then the number of reservoirs required is large, but the encoding scheme is simple
Solution Approach 1:
By enabling linker sections to encode data alongside symbol sections, the patent reduces the total number of unique oligo sequences needed in reservoirs. Since linkers carry data information, fewer distinct symbol section variants are required to represent the same data capacity, thereby reducing reservoir count while maintaining encoding capability.
Solution Approach 2:
The patent changes the encoding parameter from 'symbol section nucleotide sequence only' to 'both symbol and linker section nucleotide sequences'. This parameter expansion allows the system to achieve the same or greater data capacity with fewer reservoirs, as each reservoir contributes to multiple encoding positions in the final DNA strand.
3Quantity of substance
If DNA storage uses extended encoding with linker sections, then the information density increases four times, but the decoding complexity increases
Solution Approach 1:
The patent segments the DNA strand into alternating symbol and linker sections with defined boundaries. This segmentation allows the decoding process to systematically extract data from each section type in sequence, managing complexity through structured parsing rather than attempting to decode the entire strand as a single unit.
Solution Approach 2:
The patent introduces intermediary marker sequences or boundary motifs that delimit symbol and linker sections. These intermediaries facilitate the decoding process by providing clear transition points, allowing decoders to switch between decoding modes (symbol vs. linker encoding schemes) without confusion, thereby managing the increased complexity through structured intermediaries.
Data Source
AI summary
A system may receive, in a data read request, a DNA subsection identifier identifying a subsection of a synthesized DNA strand. The system may identify, in the subsection of the DNA strand: a first linker nucleotide subsequence (L1S) corresponding to a first end section at which the subsection was synthesized to an anterior subsection of the synthesized DNA strand, and a central nucleotide subsequence (CS) corresponding to at least a part of a central section that separates the first end section from a second end section of the subsection at which subsection was synthesized to a posterior subsection of the synthesized DNA strand. The system may determine, based on one or more nucleotides of the CS and one or more nucleotides of the L1S, data responsive to the data read request. The system may provide, responsive to the data read request, the data.