Polynucleotide Storage: Whole-Pool Amplification for Random Access
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Solution Overview
Problem
Conventional data storage technologies are unable to keep pace with exponentially growing data volumes, and existing DNA data storage methods face challenges in coding and random access, limiting the efficient retrieval of digital data stored in synthetic polynucleotides.
Innovation Solution
A framework is provided for encoding digital data in polynucleotides, using segmented polynucleotide sequences with group identifiers and universal primers, enabling selective amplification and sequencing to achieve random access by combining these processes in a single method.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Quantity of substance
If conventional data storage technologies are used, then current storage capacity is maintained, but they cannot keep pace with exponentially growing amounts of data
Solution Approach 1:
The patent uses DNA synthesis to create physical copies of digital data in molecular form, enabling massive parallel replication and storage. Each DNA molecule serves as a copy of the encoded information, allowing exponential storage capacity growth that outpaces conventional technologies.
2Quantity of substance
If DNA data storage is implemented, then information density increases to 10^18 B/mm³, but technical challenges arise in coding and random access
Solution Approach 1:
The patent segments DNA sequences into distinct functional regions including addressable tags, data payload regions, and error correction codes. This segmentation enables systematic random access by allowing specific DNA molecules to be identified and retrieved through their unique address tags without processing the entire pool.
Solution Approach 2:
The patent introduces addressable DNA tags as intermediaries between the digital data and the physical DNA storage medium. These tags enable indexing and retrieval operations by serving as searchable identifiers that mediate access to the encoded data without requiring direct manipulation of the entire DNA pool.
3Loss of information
If sequencing methods are used to retrieve data, then digital data can be decoded, but the process is destructive requiring multiple copies
Solution Approach 1:
The patent performs preliminary amplification of DNA sequences using PCR or other replication methods before sequencing occurs. This creates sufficient copies of the target DNA molecules in advance, ensuring that enough material remains after destructive sequencing to maintain the storage pool and enable future retrieval operations.
4Ease of operation
If separate amplification and sequencing procedures are used, then random access can be achieved, but unnecessary latency and complexity increase
Solution Approach 1:
The patent merges the amplification and sequencing operations into a single integrated workflow where PCR amplification is directly coupled with sequencing in one continuous process. This eliminates the latency and complexity associated with separate procedures while maintaining the ability to selectively access and retrieve specific DNA molecules from the storage pool.
Applied Scientific Principles
This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.
Function Achieved in This Case
This approach minimizes inefficiencies in retrieving digital data from polynucleotide storage systems by allowing direct access to requested data without unnecessary latency, ensuring high fidelity and efficiency in data retrieval.
Implementation Method 1
primers that are complementary to the group identifiers can be identified and used in the amplification processes
Implementation Method 2
the polynucleotides that encode the digital data being requested can be selectively amplified
Implementation Method 3
nucleotide sequencing is used to facilitate random access of the selected sequences
Data Source
AI summary
This disclosure describes an efficient method to copy all polynucleotides encoding digital data of digital files in a polynucleotide storage container while maintaining random access capabilities over a collection of files or data items in the container. The disclosure further describes a process whereby random-access and sequencing of the polynucleotides are combined in a single step.