Oligonucleotide Codeword Stack Assembly for Nucleic Acid Data Storage
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Solution Overview
Problem
Current methods for synthesizing nucleic acid strands for data storage are inefficient and costly, as they require the chemical synthesis of new oligonucleotides to construct arbitrary data strands, which is time-consuming and resource-intensive.
Innovation Solution
A system and method for efficient assembly of oligonucleotides for nucleic acid-based data storage, where a codeword stack of nucleic acid strands is synthesized initially, and codeword oligonucleotides are generated and concatenated to form a target nucleic acid data strand using techniques like PCR or Golden Gate assembly, reducing the need for new oligonucleotide synthesis.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If chemical synthesis of new oligonucleotides is used to construct arbitrary data strands, then data storage capability is achieved, but time consumption and resource usage increase significantly
Solution Approach 1:
The patent pre-synthesizes a codeword stack containing all possible codeword oligonucleotides before data encoding. When data needs to be stored, the system simply selects and assembles pre-existing oligonucleotides from the stack rather than synthesizing new ones, dramatically reducing synthesis time and resource consumption.
Solution Approach 2:
Instead of creating new oligonucleotide sequences through chemical synthesis, the patent copies and assembles existing codeword oligonucleotides from a pre-synthesized stack. This copying approach maintains data storage capability while eliminating the time-consuming synthesis step.
2Productivity
If chemical synthesis of new oligonucleotides is performed for each data strand, then arbitrary data can be encoded, but cost and resource consumption increase
Solution Approach 1:
All possible codeword oligonucleotides are synthesized in advance and stored in a codeword stack. This preliminary synthesis eliminates the need for repeated chemical synthesis operations, reducing both resource consumption and time requirements for subsequent data encoding operations.
Solution Approach 2:
The pre-synthesized codeword stack serves multiple functions: it contains all possible codewords for data encoding, provides a reusable library for assembling different data strands, and eliminates the need for repeated chemical synthesis. This multi-functional resource reduces overall resource consumption across multiple data storage operations.
3Ease of operation
If traditional oligonucleotide assembly methods are used, then data strands can be constructed, but the process is resource-intensive and slow
Solution Approach 1:
The codeword stack is pre-synthesized and organized before the actual data encoding process. This preliminary preparation creates a ready-to-use library of oligonucleotides that can be quickly selected and assembled, simplifying the encoding process while dramatically increasing assembly speed.
Solution Approach 2:
The codeword stack serves as an intermediary resource between the data encoding algorithm and the physical oligonucleotide assembly process. It mediates the translation of digital data into nucleic acid sequences by providing pre-prepared building blocks, simplifying the overall process while accelerating assembly.
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 significantly reduces the time and cost of synthesizing nucleic acid strands by using existing codeword oligonucleotides, enabling faster and more efficient assembly of nucleic acid data strands with error correction capabilities.
Implementation Method 1
codeword oligonucleotides are generated and concatenated to form a target nucleic acid data strand using techniques like PCR or Golden Gate assembly
Implementation Method 2
codeword oligonucleotides are generated and concatenated to form a target nucleic acid data strand using techniques like PCR or Golden Gate assembly
Data Source
AI summary
A computer-implemented method for efficient assembly of oligonucleotides for nucleic acid based data storage includes receiving encoded data including binary data encoded into nucleic acid sequence data, and assembling a target nucleic acid data strand based on the encoded data by, concatenating one or more selected codeword oligonucleotides obtained from a codeword stack strand.