Nucleic Acid Data Encoding Using Sequence Presence-Absence Pools
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Solution Overview
Problem
Current methods for encoding digital information into nucleic acids rely on costly base-by-base synthesis, making them inefficient for commercial implementation and error-prone for data retrieval.
Innovation Solution
Encoding digital information by mapping bit-value information to the presence or absence of unique nucleic acid sequences within a pool, using combinatorial genomic strategies such as assembly of multiple nucleic acid sequences or enzymatic editing, to construct identifier libraries that represent digital data without sequential synthesis.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If base-by-base nucleic acid synthesis is used to encode digital information, then data can be stored in nucleic acid sequences, but the encoding cost becomes expensive and the process becomes time-consuming
Solution Approach 1:
The patent divides the nucleic acid sequence into multiple segments or pools, where each pool contains a subset of possible sequences. Instead of synthesizing the entire sequence base-by-base, the system segments the encoding process into multiple smaller pools that can be prepared more efficiently and combined later, reducing the overall synthesis burden and cost.
Solution Approach 2:
The patent prepares multiple pools of nucleic acid sequences in advance, where each pool contains pre-synthesized sequences that represent specific bit values. This preliminary preparation allows the actual data encoding to be performed by simply selecting and combining pre-made sequences rather than synthesizing them on-demand, significantly reducing encoding time and cost.
2Manufacturing precision
If base-by-base nucleic acid synthesis is used to encode digital information, then data can be stored accurately, but the encoding time becomes excessively long
Solution Approach 1:
The patent segments the nucleic acid sequence into multiple pools, allowing parallel preparation of sequence subsets. This segmentation enables simultaneous synthesis and preparation of multiple sequence pools, dramatically reducing the total encoding time while maintaining accuracy through systematic combination of the segmented pools.
Solution Approach 2:
The patent performs preliminary preparation of multiple nucleic acid sequence pools in advance, creating a library of pre-synthesized sequences ready for immediate use. This preliminary action eliminates the need for time-consuming on-demand synthesis during the actual encoding process, reducing encoding time while preserving data accuracy through verified pre-synthesized sequences.
3Adaptability or versatility
If de novo nucleic acid synthesis is performed for each data encoding operation, then unique sequences can be generated, but the process becomes costly and commercially unviable
Solution Approach 1:
The patent performs preliminary synthesis of comprehensive pools of nucleic acid sequences that can be reused for multiple encoding operations. Instead of performing de novo synthesis for each data encoding, the system prepares pools in advance that contain diverse sequences representing different bit values, making subsequent encoding operations simply matter of selection and combination, thereby achieving commercial viability while maintaining sequence uniqueness.
Solution Approach 2:
The patent creates multiple copies of nucleic acid sequences within pools, where each pool contains numerous copies of sequences representing specific bit values. This copying approach allows the same verified sequences to be reused across multiple encoding operations, eliminating the need for expensive de novo synthesis for each operation while maintaining data integrity through identical verified sequences.
4Ease of operation
If sequential base-by-base synthesis is used, then complete nucleic acid sequences can be constructed, but the complexity of the encoding process increases
Solution Approach 1:
The patent divides the complex task of constructing complete nucleic acid sequences into manageable segments organized in multiple pools. Each pool contains sequences of specific segments, and the overall sequence is constructed by combining these pre-organized segments. This segmentation reduces the operational complexity by breaking down the encoding process into simpler, more manageable steps that can be performed and verified independently.
Data Source
AI summary
Methods and systems for encoding digital information in nucleic acid (e.g., deoxyribonucleic acid) molecules without base-by-base synthesis, by encoding bit-value information in the presence or absence of unique nucleic acid sequences within a pool, comprising specifying each bit location in a bit-stream with a unique nucleic sequence and specifying the bit value at that location by the presence or absence of the corresponding unique nucleic acid sequence in the pool. But, more generally, specifying unique bytes in a bytestream by unique subsets of nucleic acid sequences. Also disclosed are methods for generating unique nucleic acid sequences without base-by-base synthesis using combinatorial genomic strategies (e.g., assembly of multiple nucleic acid sequences or enzymatic-based editing of nucleic acid sequences).