Methods for retrievable information storage using nucleic acids

Patent metadata

Field	Value
Publication number	US-10289801-B2
Application number	US-201715669054-A
Country	US
Kind code	B2
Filing date	Aug 4, 2017
Priority date	Jul 13, 2015
Publication date	May 14, 2019
Grant date	May 14, 2019

Abstract

A method of storing information using monomers such as nucleotides is provided including converting a format of information into a plurality of bit sequences of a bit stream with each having a corresponding bit barcode, converting the plurality of bit sequences to a plurality of corresponding oligonucleotide sequences using one bit per base encoding, synthesizing the plurality of corresponding oligonucleotide sequences on a substrate having a plurality of reaction locations, and storing the synthesized plurality of corresponding oligonucleotide sequences.

First claim

What is claimed is:

1. A method of storing information using nucleotides comprising converting information in a first format to a plurality of bit sequences as a second format, converting the plurality of bit sequences to a plurality of corresponding oligonucleotide sequences using one bit per base encoding, synthesizing the plurality of corresponding oligonucleotide sequences by pulsing and synchronizing, nucleotides, reagents and washes across a plurality of reaction locations, and storing the synthesized plurality of corresponding oligonucleotide sequences wherein the synthesized oligonucleotide sequences are formed using a template independent polymerase and a selected nucleotide under conditions to catalyze addition of the selected nucleotide.

2. The method of claim 1 wherein the synthesized plurality of oligonucleotide sequences include one or more or all of a data block sequence, an address sequence specifying the location of the data block in a bit stream, or flanking common sequences at each end of the oligonucleotide for amplification and sequencing.

3. The method of claim 1 comprising amplifying the synthesized plurality of oligonucleotide sequences, sequencing the amplified plurality of oligonucleotide sequences, converting the amplified plurality of oligonucleotide sequences to bit sequences, and converting the bit sequences to the information in the first format.

4. The method of claim 3 further comprising outputting the information in the first format.

5. The method of claim 1 wherein the synthesized oligonucleotide sequences are formed using a pH-sensitive template independent polymerase and a selected nucleotide under conditions to catalyze addition of the selected nucleotide.

6. The method of claim 1 wherein the synthesized oligonucleotide sequences are formed using a light-sensitive template independent polymerase and a selected nucleotide under conditions to catalyze addition of the selected nucleotide.

7. The method of claim 1 wherein the synthesized oligonucleotide sequences are attached to a substrate.

8. The method of claim 1 wherein the information in the first format is a text, image, video or audio format of information.

9. The method of claim 1 wherein the nucleotides are natural nucleotides.

10. The method of claim 1 wherein the synthesized oligonucleotide sequences are greater than 100 nucleotides, 500 nucleotides, or 1000 nucleotides.

11. The method of claim 1 wherein the synthesized oligonucleotide sequences are formed using terminal deoxynucleotidyl transferase and a selected nucleotide under conditions to catalyze addition of the selected nucleotide.

12. The method of claim 1 wherein the synthesized oligonucleotide sequences are formed by forming an extension product using a template independent polymerase, one or more of Co 2+ , Mn 2+ , Zn 2+ and Mg 2+ , and a nucleotide under conditions to catalyze addition of the nucleotide to form a growing polymer chain attached to a substrate.

13. The method of claim 1 wherein the plurality of reaction locations include single stranded nucleic acid initiator sequences that are repeatedly extended with nucleotides using a template independent polymerase, one or more of Co 2+ , Mn 2+ , Zn 2+ and Mg 2+ , and nucleotides under conditions to catalyze addition of the nucleotides to form growing polymer chains attached to a substrate.

14. The method of claim 1 wherein the plurality of reaction locations include single stranded nucleic acid initiator sequences that are repeatedly extended with nucleotides using a template independent polymerase, one or more of Co 2+ , Mn 2+ , Zn 2+ and Mg 2+ , and nucleotides under conditions to catalyze addition of the nucleotides to form growing polymer chains attached to a substrate to produce an array of predetermined sequences at corresponding known locations.

15. The method of claim 1 wherein the plurality of reaction locations include single stranded nucleic acid initiator sequences that are repeatedly extended with nucleotides using a template independent polymerase, one or more of Co 2+ , Mn 2+ , Zn 2+ and Mg 2+ , and nucleotides under conditions to catalyze addition of the nucleotides to form growing polymer chains attached to a substrate to produce an array of predetermined sequences at corresponding known locations, wherein the array includes at least 10 2 , 10 3 , 10 4 , 10 5 , 10 6 , 10 7 , 10 8 , 10 9 , 10 10 predetermined sequences each at corresponding known regions.

16. The method of claim 1 wherein the synthesized oligonucleotide sequences are produced by limiting reaction time of the nucleotide by adding nucleotide depleted buffer to remove the nucleotide thereby limiting its reaction time or by limiting a pulse rate of a flow of the nucleotide at a reaction location.

17. The method of claim 1 wherein each bit sequence comprises a corresponding bit barcode.

18. The method of claim 1 wherein the plurality of reaction locations are on a substrate surface.

19. The method of claim 1 wherein each bit sequence comprises a corresponding bit barcode and the plurality of reaction locations are on a substrate surface.

Assignees

• Harvard College

Inventors

• Church George M

Classifications

• G16B50/00 Primary

  ICT programming tools or database systems specially adapted for bioinformatics · CPC title

• B01J2219/00608

  DNA chips · CPC title

• C12Q1/6874

  involving nucleic acid arrays, e.g. sequencing by hybridisation · CPC title

• G06F5/08

  having a sequence of storage locations, the intermediate ones not being accessible for either enqueue or dequeue operations, e.g. using a shift register {(G06F5/065 takes precedence; shift registers per se G11C19/00)} · CPC title

• C12Q1/68

  involving nucleic acids · CPC title