# US 2020/0401903 A1 · Nucleic acid-based data storage

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- Number: US 2020/0401903 A1
- Document ID: US20200401903A1
- Status: Published application
- Kind: A1
- Application number: 17/007,946
- Filed: 2020-08-31
- Published: 2020-12-24
- Earliest claimed: 2016-11-16
- Assignees: Catalog Technologies, Inc.
- Applicants: Catalog Technologies, Inc.
- Inventors: Nathaniel Roquet; Hyunjun Park; Swapnil P. Bhatia
- Web page: https://patentgrep.com/patent/US20200401903A1

## 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 at position 1

1-29. (canceled)

### Claim 30

A method for writing information into nucleic acid sequences, the method comprising:
translating the information into a string of symbols;
mapping the string of symbols to a plurality of identifiers, wherein each individual identifier of the plurality of identifiers corresponds to a unique nucleic acid sequence and comprises a corresponding plurality of components, wherein each component of the plurality of components comprises a distinct nucleic acid sequence, and wherein each identifier corresponds to an individual symbol in the string of symbols; and
forming at least one individual identifier of the plurality of identifiers by depositing the corresponding plurality of components into a compartment, wherein the plurality of components assemble via one or more reactions in the compartment to form the at least one individual identifier.

### Claim 31 (depends on 30)

The method of claim 30, wherein each symbol is one of two possible symbol values.

### Claim 32 (depends on 31)

The method of claim 31, wherein a first symbol value of the two possible symbol values is represented by an absence of a distinct identifier of the plurality of identifiers, and wherein a second symbol value of the two possible symbol values is represented by a presence of the distinct identifier, or vice versa.

### Claim 33 (depends on 32)

The method of claim 32, wherein the two or more components assemble via the one or more reactions to form identifiers that each correspond to symbols having symbol values that are represented by the presence of the corresponding distinct identifiers.

### Claim 34 (depends on 30)

The method of claim 30, wherein the distinct nucleic acid sequence of each individual component is non-specific to any individual symbol.

### Claim 35 (depends on 30)

The method of claim 30, wherein each component comprises a distinct nucleic acid sequence with first and second ends, a first hybridization region on the first end, and a second hybridization region on the second end.

### Claim 36 (depends on 30)

The method of claim 30, wherein each of the plurality of components belongs in one of M layers, and wherein one component from each of the M layers assemble to form the at least one identifier.

### Claim 37 (depends on 36)

The method of claim 36, wherein each layer of the M layers comprises a distinct set of components.

### Claim 38 (depends on 37)

The method of claim 37, wherein within each layer, the components have a common first hybridization region and a common second hybridization region.

### Claim 39 (depends on 30)

The method of claim 30, wherein each component in the compartment has first and second hybridization regions, and the first or second hybridization region of each component is complementary to the first or second hybridization region of another component, and wherein the one or more reactions comprise hybridization of the first and second complimentary hybridization regions.

### Claim 40 (depends on 30)

The method of claim 30, wherein the one or more components assemble in a non-order dependent manner.

### Claim 41 (depends on 30)

The method of claim 30, wherein a subset of the plurality of identifiers are formed via one reaction in a multiplex fashion.

### Claim 42 (depends on 30)

The method of claim 30, wherein the one or more reactions comprise overlap-extension polymerase chain reaction (PCR), polymerase cycling assembly, sticky end ligation, ligase cycling reaction, or template directed ligation.

### Claim 43 (depends on 30)

The method of claim 30, further comprising generating an identifier library comprising the at least one formed identifier.

### Claim 44 (depends on 43)

The method of claim 43, wherein the identifier library comprises a distinct barcode, metadata of the information, or both.

### Claim 45 (depends on 44)

The method of claim 44, further comprising extracting a targeted subset of the identifier library.

### Claim 46 (depends on 45)

The method of claim 45, further comprising combining a plurality of probes with the identifier library, wherein the plurality of probes share complementarity with the one or more components of each identifier of the targeted subset such that each identifier of the targeted subset hybridizes with at least one probe when combined with the plurality of probes.

### Claim 47 (depends on 46)

The method of claim 46, wherein the plurality of probes comprises one or more affinity tags, and wherein the one or more affinity tags are captured by an affinity bead or an affinity column.

### Claim 48 (depends on 45)

The method of claim 45, wherein each identifier comprises one or more common primer binding regions, one or more variable primer binding regions, or any combination thereof.

### Claim 49 (depends on 48)

The method of claim 48, further comprising:
combining the identifier library with primers that bind to the one or more common primer binding regions or to the one or more variable primer binding regions, wherein the primers bind to the one or more common primer binding regions or to the one or more variable primer binding regions; and
selectively amplifying said targeted subset of said identifier library.

### Claim 50 (depends on 45)

The method of claim 45, further comprising selectively removing a portion of non-targeted identifiers from said identifier library.