Systems for nucleic acid-based data storage
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).
1. A method for coding digital information into nucleic acid sequence(s), comprising:
(a) coding said digital information into a sequence of symbols and converting said sequence of symbols into codewords;
(b) parsing said codewords into a coded sequence of symbols;
(c) mapping said coded sequence of symbols to a plurality of identifiers, wherein an individual identifier of said plurality of identifiers comprises one or more nucleic acid sequences;
(d) enumerating an identifier library wherein each symbol of said coded sequence of symbols is encoded by one or more identifier(s); and
(e) ordering the identifiers of the identifier library.
2. The method of claim 1 , wherein the coding comprises coding using one or more codebooks.
3. The method of claim 1 , wherein said coded sequence of symbols comprises symbols taken from a fixed alphabet of symbols.
4. The method of claim 1 , comprising appending one or more error protection symbols to the sequence of symbols.
5. The method of claim 1 , wherein said coded sequence of symbols comprises one or more blocks of symbols.
6. The method of claim 1 , wherein converting said sequence of symbols into a sequence of codewords generates a fixed number of one or more types of symbols in each block of symbols of said one or more blocks of symbols.
7. The method of claim 6 , wherein a codebook appends one or more error protection symbols to individual codewords of said sequence of codewords.
8. The method of claim 1 , wherein said plurality of identifiers are selected from a combinatorial space of identifiers.
9. The method of claim 1 , wherein an individual identifier of said plurality of identifiers comprises one or more components.
10. The method of claim 9 , wherein an individual component of said one or more components comprises a nucleic acid sequence.
11. The method of claim 10 , wherein said nucleic acid sequence is a distinct sequence.
12. The method of claim 1 , wherein said identifier library comprises supplemental nucleic acid sequences.
13. The method of claim 12 , wherein said supplemental nucleic acid sequences comprise metadata about said first sequence of symbols or an encoding of said first sequence of symbols.
14. The method of claim 12 , wherein said supplemental nucleic acid sequences do not correspond to digital information.
15. The method of claim 1 , wherein said one or more identifier(s) are generated by combinatorial assembly of one or more components.
16. The method of claim 1 , further comprising constructing a universal identifier library.
17. The method of claim 16 , wherein constructing said universal identifier library comprises using one or more reactions.
18. The method of claim 17 , wherein said one or more reactions comprise components, templates, and/or reagents.
19. The method of claim 1 , comprising reading a sample of identifiers, wherein reading comprises using molecular biology methods.
20. The method of claim 19 , wherein the molecular biology method comprises PCR.