Spatially Layered DNA Storage for Real-Time Oligo Pool Readout
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Current DNA data storage methods based on oligo pools face challenges with high synthesis and sequencing times, and inefficiencies in error correction due to base insertion/deletion errors, limiting real-time data reading and recovery.
Innovation Solution
A spatially layered DNA storage method that integrates error correction encoding, base run-length sequence merging, and real-time coding, using high-throughput sequencing to achieve real-time data readout by grouping data into layers, adding indices and primers, and employing feedback mechanisms to correct insertion/deletion errors.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If next-generation high-throughput sequencing is used for DNA data storage readout, then data can be read sequentially after complete sequencing, but the sequencing process is time-consuming and cannot achieve real-time readout
Solution Approach 1:
The patent divides the DNA sequence into multiple independent layers, where each layer can be read and decoded separately. This segmentation allows partial data recovery without requiring complete sequencing of the entire DNA molecule, significantly reducing the time needed for data readout while maintaining sequencing accuracy through targeted analysis of specific layers.
Solution Approach 2:
The patent performs preliminary encoding by organizing data into layered structures with embedded indices and primers before sequencing. This preliminary organization enables the sequencing system to quickly identify and read specific layers without processing the entire sequence, achieving real-time readout capability while maintaining accurate measurement through pre-structured data architecture.
2Reliability
If conventional error correction codes are used in DNA storage, then they can correct substitution errors, but they are ineffective against base insertion/deletion errors that disrupt the entire strand
Solution Approach 1:
The patent segments the DNA storage system into multiple independent layers, where each layer is protected by its own error correction code. This segmentation isolates insertion/deletion errors to specific layers, preventing them from disrupting the entire strand. Conventional error correction codes can then effectively correct errors within each layer without being overwhelmed by strand-wide disruptions.
Solution Approach 2:
The patent introduces a vertical dimension to error correction by organizing data into layered structures. Instead of relying solely on horizontal error correction across the entire strand, the system provides error protection in the vertical dimension through layer-specific codes, enabling versatile error correction that handles both substitution and insertion/deletion errors effectively.
3Productivity
If spatially layered encoding is implemented, then real-time readout and error correction are enabled, but the encoding and decoding process complexity increases
Solution Approach 1:
The patent performs preliminary organization of data into layered structures with embedded indices and primers during the encoding phase. This preliminary action simplifies the decoding process by pre-establishing the hierarchical structure, allowing the system to quickly navigate and read specific layers without complex real-time computations, thus achieving real-time readout while managing encoding complexity through structured preparation.
Solution Approach 2:
The patent implements feedback mechanisms where decoding results from one layer inform the reading process of subsequent layers. This feedback approach optimizes the decoding complexity by using information from successfully decoded layers to guide the interpretation of remaining layers, reducing the overall computational burden while maintaining high productivity through iterative refinement.
4Quantity of substance
If large-scale oligo pools are used for high-density storage, then storage capacity increases, but synthesis costs and sequencing time increase proportionally
Solution Approach 1:
The patent divides large-scale oligo pools into multiple manageable layers, where each layer represents a subset of the total data. This segmentation allows the system to process and sequence individual layers independently, reducing the time required for synthesis and sequencing compared to processing the entire large-scale pool as a single unit, while still achieving high storage capacity through the aggregation of multiple layers.
Solution Approach 2:
The patent enables partial reading of data layers, allowing the system to retrieve information from specific layers without sequencing the entire oligo pool. This partial action approach significantly reduces sequencing time and synthesis costs by focusing only on the necessary data layers, while the underlying architecture maintains the capacity for high-density storage when full data retrieval is required.
Data Source
AI summary
The present disclosure discloses a spatially layered DNA storage method for large-scale oligonucleotide pools, employing a DNA spatially layered coding method to enable real-time data readout; the unordered DNA strands are spatially organized into an addressable base array, and the live data are encoded chronologically into sequential coding layers, wherein bases are mapped to crosscutting identical positions across all strands; for recovery, a live and accelerated approach to spatially form a coding layer is provided, and the error correction codes are utilized to fill the base gap, enabling continuous, real-time streaming; a layer-wise spatial-temporal recovery method is presented to facilitate an error-free data stream, spatially achieving instant consensus of multiple signals within a layer, and temporally updating flow signals via the previous successfully decoded layers; the error correction and readout methods provided by the present disclosure can match the sequencing process, achieving simultaneous sequencing and real-time decoding.