DNA data storage using reusable nucleic acids

Patent metadata

Field	Value
Publication number	US-10838939-B2
Application number	US-201715796131-A
Country	US
Kind code	B2
Filing date	Oct 27, 2017
Priority date	Oct 28, 2016
Publication date	Nov 17, 2020
Grant date	Nov 17, 2020

Abstract

Disclosed herein are nucleic acid-based data storage systems and nucleic acid data storage constructs comprising reusable nucleic acid sequences, each representing information carried by a single bit (and, in some embodiments, one or more adjacent bits) within a bit string, and each furthermore representing the position of the single bit within the bit string. Also described are methods for storing data in the nucleic acid-based data storage systems and nucleic acid data storage constructs of the disclosure.

First claim

What is claimed is:

1. A collection of data storage nucleic acids comprising:
a plurality of data storage nucleic acids, each data storage nucleic acid comprising one of N different bit-mer sequences,
wherein each bit-mer sequence represents information carried by a single bit in a primary bit string n bits in length,
wherein each bit-mer sequence represents a position of the single bit within the primary bit string, and
wherein:
(i) N equals n where the primary bit string is a binary bit string, wherein each data storage nucleic acid comprising one of N different bit-mer sequences can be present or absent in the collection of data storage nucleic acids, and wherein the presence of a data storage nucleic acid comprising a particular bit-mer sequence denotes a 1 and the absence of data storage nucleic acid comprising a particular a bit-mer sequence denotes a 0 at a particular position within the primary bit string, or vice versa;
(ii) N equals 2·n where the primary bit string is a binary bit string, and where each of n bit-mer sequences denote a 1 at a particular position within the primary bit string and each of the other n bit-mer sequences denote a 0 at a particular position within the primary bit string; and
(iii) N equals B·n where the primary bit string is a base-B bit string where B is greater than 2, and where each of B·n bit-mer sequences represents a particular base-B digit at a particular position within the primary bit string.

2. The collection of data storage nucleic acids of claim 1 , each data storage nucleic acid further comprising one of x secondary positional indices, each secondary positional index comprising one or more secondary positional index nucleic acid sequences,
wherein the data storage nucleic acids that represent bits from the same primary bit string all comprise the same secondary positional index, and
wherein each secondary positional index represents the position of one of x primary bit strings relative to other primary bit strings within a secondary bit string x times n bits in length.

3. The collection of data storage nucleic acids of claim 2 , each data storage nucleic acid further comprising one of y tertiary positional indices, each tertiary positional index comprising one or more tertiary positional index nucleic acid sequences,
wherein the data storage nucleic acids that represent bits from the same secondary bit string all comprise the same tertiary positional index, and
wherein each tertiary positional index represents the position of one of y secondary bit strings relative to other secondary bit strings within a tertiary bit string x times y times n bits in length.

4. The collection of data storage nucleic acids of claim 1 , each data storage nucleic acid further comprising a document identification sequence and a document-specific primer binding sequence,
wherein the data storage nucleic acids that represent bits from the same document all comprise the same document identification sequence and document-specific primer binding sequence.

5. The collection of data storage nucleic acids of claim 4 , each data storage nucleic acid further comprising a folder identification sequence and a folder-specific primer binding sequence,
wherein the data storage nucleic acids that represent bits from one or more documents in the same folder all comprise the same folder identification sequence and folder-specific primer binding sequence.

6. The collection of data storage nucleic acids of claim 4 , each data storage nucleic acid further comprising a page recognition sequence,
wherein the data storage nucleic acids that represent bits from the same page within a document all comprise the same page recognition sequence, and
wherein the page recognition sequence, together with the document identification sequence and document-specific primer binding sequence, forms a primer binding site allowing data storage nucleic acids sharing a single page recognition sequence to be selectively amplified from the collection together.

7. The collection of data storage nucleic acids of claim 1 , wherein B is 256 such that the primary bit string is a base-256 bit string and each bit-mer sequence represents a byte of information.

8. A method for storing data in a collection of data storage nucleic acids, the method comprising:
(a) converting the data into a base-B bit string;
(b) sub-dividing the base-B bit string into y secondary bit strings, and sub-dividing each secondary bit string into x primary bit strings n bits in length;
(c) for each of x primary bit strings:
(i) performing one of:
(A) where B equals 2, such that the base-B bit string is a binary bit string, from a library of n primary data storage nucleic acids, each comprising a single bit-mer sequence, each bit-mer sequence representing a specific position of a primary bit string n bits in length, selecting the primary data storage nucleic acid with the bit-mer sequence for each position of the primary bit string which is a 1, and selecting no primary data storage nucleic acid for each position of the primary bit string which is a 0;
(B) where B equals 2, such that the base-B bit string is a binary bit string, from a library of 2·n primary data storage nucleic acids, each comprising a single bit-mer sequence, each of n bit-mer sequences representing a 1 at a specific position of a primary bit string n bits in length, and each of n other bit-mer sequences representing a 0 at a specific position of the primary bit string, selecting the primary data storage nucleic acid with the 1 bit-mer sequence for each position of the primary bit string which is a 1, and selecting the primary data storage nucleic acid with the 0 bit-mer sequence for each position of the primary bit string which is a 0; or
(C) where B is greater than 2, from a library of B·n primary data storage nucleic acids, each comprising a single bit-mer sequence, each of B·n bit-mer sequences representing a particular base-B digit at a specific position of the primary bit string, selecting the primary data storage nucleic acid with the appropriate bit-mer sequence for each position of the primary bit string;
wherein all primary data storage nucleic acids comprise the same 5′ and 3′ 1° primer binding sequences flanking the bit-mer sequence therein;

(ii) pooling the selected data storage nucleic acids to form one of x pools of primary data storage nucleic acids storing the data of one of x primary bit strings;
(iii) using a 1° primer pair that binds to the 5′ and 3′ 1° primer binding sequences to add to each primary data storage nucleic acid the same 5′ and 3′ secondary positional index sequences and, optionally, the same 5′ and 3′ 2° primer binding sequences to produce a pool of secondary data storage nucleic acids,
wherein each of x pools of secondary data storage nucleic acids comprise different 5′ and 3′ secondary positional index sequences; and

(d) pooling the x pools of secondary data storage nucleic acids corresponding to the x primary bit strings within each of y secondary bit strings into a single pool, to form y pools of secondary data storage nucleic acids, each storing the data of one of y secondary bit strings.

9. The method of claim 8 , wherein the base-B bit string is instead sub-divided into z tertiary bit strings, each tertiary bit string sub-divided into y secondary bit strings, and each secondary bit string sub-divided into x primary bit strings n bits in length, the method further comprising:
(e) for each of y pools of secondary data storage nucleic acids, using a 2° primer pair that binds to the 5′ and 3′ 2° primer binding sequences to add to each secondary data storage nucleic acid the same 5′ and 3′ tertiary positional index sequences;
optionally, the same 5′ an

Assignees

• Integrated Dna Tech Inc

Inventors

• Walder Joseph Alan
• Manthey Jeffrey A
• Martin Iii William E
• Allen Shawn

Classifications

• G16B50/30

  Data warehousing; Computing architectures · CPC title

• G06N3/123 Primary

  DNA computing · CPC title

• G16B30/00

  ICT specially adapted for sequence analysis involving nucleotides or amino acids · CPC title

• G06F16/2237 Primary

  Vectors, bitmaps or matrices · CPC title

• G06F16/2272

  Management thereof · CPC title