Nucleic Acid Text Encoding via Custom Codon Mapping
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Solution Overview
Problem
Conventional encoding schemes for storing human readable information in nucleic acid sequences face challenges such as potential biological impact on cells and inefficiency, often relying on codon-redundancy and requiring knowledge of the carrier gene's sequence, which limits message length and efficiency.
Innovation Solution
A novel encoding scheme that translates human readable symbols into codon identifiers, specifically designed to minimize biological impact by using a low probability of transcription or translation, allowing for efficient storage with a low probability of biological effect and enabling decoding without prior knowledge of the gene's structure or function.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Quantity of substance
If conventional encoding schemes use codon-redundancy to store human readable information in nucleic acid sequences, then storage capacity is achieved, but biological impact on cells increases and decoding requires prior knowledge of the carrier gene's sequence
Solution Approach 1:
The patent changes the encoding parameters by using a custom codon table with non-standard codon assignments rather than the natural genetic code. This allows efficient storage of human readable information while using codons that have low probability of being transcribed or translated by cellular machinery, thereby reducing biological impact on the host cell
Solution Approach 2:
The patent introduces a custom codon table as an intermediary layer between human readable information and nucleic acid sequences. This codon table serves as a translation dictionary that enables efficient encoding without relying on the natural genetic code, thus avoiding biological impact while maintaining storage capacity
2Quantity of substance
If conventional encoding schemes rely on codon-redundancy, then storage is enabled, but decoding complexity increases due to requirement of carrier gene sequence knowledge
Solution Approach 1:
The custom codon table acts as a self-contained intermediary that contains all necessary decoding information. The decoder simply needs to apply the same custom codon table used during encoding, without requiring any knowledge of the carrier gene's natural sequence or structure, thus simplifying the decoding process
Solution Approach 2:
The patent segments the decoding process into two independent components: the custom codon table (encoding/decoding key) and the nucleic acid sequence. This segmentation allows the decoder to operate independently of the carrier gene's biological characteristics, reducing decoding complexity
3Reliability
If encoding schemes use standard genetic code, then biological viability is maintained, but information storage efficiency decreases
Solution Approach 1:
The patent changes the codon assignment parameters by creating a custom codon table where codons are assigned to encode human readable information rather than amino acids. This optimization prioritizes information storage efficiency while selecting codons with low transcription/translation probability to maintain biological viability
Solution Approach 2:
The patent applies local quality by making the codon assignments specific to the encoding purpose rather than universal. The custom codon table is tailored for information storage in specific nucleic acid contexts, allowing efficient encoding in those local contexts while maintaining overall biological compatibility
Data Source
AI summary
Methods and apparatus are disclosed herein for encoding human readable text conveying a non-genetic message into nucleic acid sequences with a substantially reduced probability of biological impact and decoding such text from nucleic acid sequences. In one embodiment, each symbol of a symbol set of human readable symbols uniquely maps to a respective codon identifier. Mapping may ensure that each symbol will not map to a codon identifier that generates an amino acid residue which has a single-letter abbreviation that is the equivalent to the respective symbol. Synthetic nucleic acid sequences comprising such human readable text, and recombinant or synthetic cells comprising such sequences are provided, as well as methods of identifying cells, organisms, or samples containing such sequences.