# US 12,001,962 B2 · Systems for nucleic acid-based data storage

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- Number: US 12,001,962 B2
- Document ID: US12001962B2
- Status: Granted
- Kind: B2
- Application number: 18/230,273
- Filed: 2023-08-04
- Published: 2024-01-11
- Granted: 2024-06-04
- Earliest claimed: 2016-11-16
- Assignees: Catalog Technologies, Inc.
- Applicants: Catalog Technologies, Inc.
- Inventors: Nathaniel Roquet; Hyunjun Park; Swapnil P. Bhatia; Darren R. Link
- Web page: https://patentgrep.com/patent/US12001962B2

## CPC

- G06N 3/123: DNA computing
- C12N 9/22: Ribonucleases {[RNase]; Deoxyribonucleases [DNase]}
- C12N 15/1031: {mutagenesis by gene assembly, e.g. assembly by oligonucleotide extension PCR}
- C12N 15/1089: {Design, preparation, screening or analysis of libraries using computer algorithms}
- C40B 50/06: Biochemical methods, e.g. using enzymes or whole viable microorganisms
- G06F 16/2272: {Management thereof}
- G06F 16/245: Query processing
- G11C 13/0019: {comprising bio-molecules}
- G16B 25/20: Polymerase chain reaction [PCR]; Primer or probe design; Probe optimisation
- G16B 30/00: ICT specially adapted for sequence analysis involving nucleotides or amino acids
- G16B 30/20: Sequence assembly
- G16B 50/00: ICT programming tools or database systems specially adapted for bioinformatics
- G16B 50/30: Data warehousing; Computing architectures
- G16B 99/00: Subject matter not provided for in other groups of this subclass
- H03M 7/40: Conversion to or from variable length codes, e.g. Shannon-Fano code, Huffman code, Morse code
- C12N 2310/20: involving clustered regularly interspaced short palindromic repeats [CRISPR]
- G06N: COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
- C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00)
- C40B: COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES (in silico combinatorial libraries of nucleic acids, proteins or peptides G16B35/00; in silico combinatorial chemistry G16C20/60)
- G06F: ELECTRIC DIGITAL DATA PROCESSING (computer systems based on specific computational models G06N)
- G11C: STATIC STORES (semiconductor memory devices H10B)
- G16B: BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- H03M: CODING; DECODING; CODE CONVERSION IN GENERAL (using fluidic means F15C4/00; optical analogue/digital converters G02F7/00; coding, decoding or code conversion, specially adapted for particular applications, see the relevant subclasses, e.g. G01D, G01R, G06F, G06T, G09G, G10L, G11B, G11C, H04B, H04L, H04M, H04N; ciphering or deciphering for cryptography or other purposes involving the need for secrecy G09C)

## Abstract

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).

## Claims

### Claim 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.

### Claim 2 (depends on 1)

The method of claim 1, wherein the coding comprises coding using one or more codebooks.

### Claim 3 (depends on 1)

The method of claim 1, wherein said coded sequence of symbols comprises symbols taken from a fixed alphabet of symbols.

### Claim 4 (depends on 1)

The method of claim 1, comprising appending one or more error protection symbols to the sequence of symbols.

### Claim 5 (depends on 1)

The method of claim 1, wherein said coded sequence of symbols comprises one or more blocks of symbols.

### Claim 6 (depends on 1)

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.

### Claim 7 (depends on 6)

The method of claim 6, wherein a codebook appends one or more error protection symbols to individual codewords of said sequence of codewords.

### Claim 8 (depends on 1)

The method of claim 1, wherein said plurality of identifiers are selected from a combinatorial space of identifiers.

### Claim 9 (depends on 1)

The method of claim 1, wherein an individual identifier of said plurality of identifiers comprises one or more components.

### Claim 10 (depends on 9)

The method of claim 9, wherein an individual component of said one or more components comprises a nucleic acid sequence.

### Claim 11 (depends on 10)

The method of claim 10, wherein said nucleic acid sequence is a distinct sequence.

### Claim 12 (depends on 1)

The method of claim 1, wherein said identifier library comprises supplemental nucleic acid sequences.

### Claim 13 (depends on 12)

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.

### Claim 14 (depends on 12)

The method of claim 12, wherein said supplemental nucleic acid sequences do not correspond to digital information.

### Claim 15 (depends on 1)

The method of claim 1, wherein said one or more identifier(s) are generated by combinatorial assembly of one or more components.

### Claim 16 (depends on 1)

The method of claim 1, further comprising constructing a universal identifier library.

### Claim 17 (depends on 16)

The method of claim 16, wherein constructing said universal identifier library comprises using one or more reactions.

### Claim 18 (depends on 17)

The method of claim 17, wherein said one or more reactions comprise components, templates, and/or reagents.

### Claim 19 (depends on 1)

The method of claim 1, comprising reading a sample of identifiers, wherein reading comprises using molecular biology methods.

### Claim 20 (depends on 19)

The method of claim 19, wherein the molecular biology method comprises PCR.