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 .- 29 . (canceled)
30 . A method for writing information into nucleic acid sequence(s), comprising:
(a) translating said information into a string of symbols;
(b) mapping said string of symbols to a plurality of identifiers, each identifier encoding a value and a position of the symbol in the string of symbols,
wherein an individual identifier of said plurality of identifiers comprises one or more components, wherein an individual component of said one or more components comprises a nucleic acid sequence; and
(c) constructing an identifier library comprising at least a subset of said plurality of identifiers by inserting at least one component into a parent identifier by applying a nucleic acid editing enzyme to said parent identifier.
31 . The method of claim 30 , wherein said parent identifier comprises a plurality of components flanked by nuclease-specific target sites, recombinase recognition sites, or distinct spacer sequences.
32 . The method of claim 30 , wherein said nucleic acid editing enzyme is selected from the group consisting of CRISPR-Cas, TALENs, Zinc Finger Nucleases, Recombinases, and functional variants thereof.
33 . The method of claim 30 , wherein one symbol value at each position of said string of symbols may be represented by the absence of a distinct identifier in the identifier library.
34 . The method of claim 30 , wherein each symbol in said string of symbols is one of two possible symbol values, said two possible symbol values being a bit-value of 0 and 1,
wherein said individual symbol with said bit-value of 0 in said string of symbols may be represented by an absence of a distinct identifier in said identifier library, wherein said individual symbol with said bit-value of 1 in said string of symbols may be represented by a presence of said distinct identifier in said identifier library, and vice versa.
35 . The method of claim 30 , wherein constructing said individual identifier in said identifier library comprises assembling said one or more components from one or more layers and wherein each layer of said one or more layers comprises a distinct set of components.
36 . The method of claim 35 , wherein said individual identifier from said identifier library comprises one component from each layer of said one or more layers.
37 . The method of claim 36 , wherein said one or more components are assembled in a fixed order.
38 . The method of claim 36 , wherein said one or more components are assembled in any order.
39 . The method of claim 36 , wherein said one or more components are assembled with one or more partitioning components disposed between two components from different layers of said one or more layers.
40 . The method of claim 35 , wherein said individual identifier comprises one component from each layer of a subset of said one or more layers.
41 . The method of claim 35 , wherein said individual identifier comprises at least one component from each of said one or more layers.
42 . The method of claim 35 , wherein said one or more components are assembled using overlap-extension polymerase chain reaction (PCR), polymerase cycling assembly, sticky end ligation, biobricks assembly, golden gate assembly, gibson assembly, recombinase assembly, ligase cycling reaction, or template directed ligation.
43 . The method of claim 30 , wherein said identifier library comprises a plurality of nucleic acid sequences.
44 . The method of claim 43 , wherein said plurality of nucleic acid sequences stores metadata of said information and/or conceals said information.
45 . The method of claim 44 , wherein said metadata comprises secondary information corresponding to a source of said information, an intended recipient of said information, an original format of said information, instrumentation and methods used to encode said information, a date and a time of writing said information into said identifier library, modifications made to said information, and/or a reference to other information.
46 . The method of claim 30 , wherein one or more identifier libraries are combined and wherein each identifier library of said one or more identifier libraries is tagged with a distinct barcode.
47 . The method of claim 46 , wherein each individual identifier in said identifier library comprises said distinct barcode.
48 . The method of claim 30 , wherein said plurality of identifiers is selected for ease of read, write, access, copy, and deletion operations.
49 . The method of claim 30 , wherein said plurality of identifiers is selected to minimize write errors, mutations, degradation, and read errors.