Nucleic acid based data storage using enzymatic bioencryption

Abstract

Provided herein are compositions, devices, systems and methods for the generation and use of secured biomolecule-based information for storage. Further described herein are compositions, devices, systems and methods for bioencryption or biodecryption of information. Conversion of a digital sequence to a nucleic based sequence includes a step of selection of one or more bioencryption methods.

1 .- 34 . (canceled) 
     
     
         35 . A method for preparing a library for use in secure retrieval of an item, the method comprising:
 a. obtaining a library of nucleic acid molecules representing an encryption nucleic acid sequence, wherein the encryption nucleic acid sequence is a known nucleic acid sequence, which when decrypted, identifies the item; and   b. applying an operation based on a bioencryption format to the library representing the encryption nucleic acid sequence to obtain a decrypted library.   
     
     
         36 . The method of  claim 35 , further comprising sequencing at least a portion of the decrypted library to generate nucleic acid sequences. 
     
     
         37 . The method of  claim 35 , further comprising performing an error correction, wherein the error correction comprises identifying one or more mismatches, bulges and small loops, chemically altered bases, or other heteroduplexes. 
     
     
         38 . The method of  claim 36 , wherein sequencing comprises next generation sequencing. 
     
     
         39 . The method of  claim 35 , further comprising enriching the decrypted library. 
     
     
         40 . The method of  claim 39 , wherein enriching comprises one or more of pull down assay using beads having complementary capture probes bound thereto, PCR using primers selected to target a sequence of the decrypted library, or size exclusion chromatography. 
     
     
         41 . The method of  claim 35 , wherein the item comprises text, audio, or visual information. 
     
     
         42 . The method of  claim 35 , wherein the item comprises a book, periodical, database, medical record, letter, form, voice recording, animal recording, biological profile, broadcast, film, short video, email, bookkeeping phone log, internet activity log, drawing, painting, print, photograph, pixelated graphic, or software code. 
     
     
         43 . The method of  claim 42 , wherein the biological profile comprises a gene library, genome, gene expression data, or protein activity data. 
     
     
         44 . The method of  claim 35 , wherein the library comprises at least 100,000 oligonucleotides. 
     
     
         45 . The method of  claim 35 , wherein the operation based on the bioencryption format comprises exposing of the plurality of oligonucleotides to one or more species. 
     
     
         46 . The method of  claim 45 , wherein the one or more species comprises an enzyme, radiation, affinity tag, or chemical species. 
     
     
         47 . The method of  claim 46 , wherein the enzyme comprises a nuclease complex. 
     
     
         48 . The method of  claim 47 , wherein the nuclease complex comprises a Cas nuclease (CRISPR associated), a Zinc Finger Nuclease (ZFN), a Transcription Activator-Like Effector Nuclease, an Argonaute nuclease, S1 Nuclease, a mung bean nuclease, or a DNAse. 
     
     
         49 . The method of  claim 47 , wherein the nuclease complex comprises an enzyme as set out in Table 1. 
     
     
         50 . The method of  claim 46 , wherein the radiation comprises electromagnetic radiation comprising a wavelength of about 0.01 nm to about 400 nm. 
     
     
         51 . The method of  claim 46 , wherein the chemical species comprises gaseous ammonia or methylamine administration. 
     
     
         52 . The method of  claim 46 , wherein the affinity tag comprises biotin, digoxigenin, Ni-Nitrilotriacetic acid, desthiobiotin, histidine, polyhistidine, myc, hemagglutinin (HA), FLAG, a fluorescence tag, a tandem affinity purification (TAP) tag, glutathione S transferase (GST), a polynucleotide, an aptamer, an antigen, or an antibody. 
     
     
         53 . A method for retrieving information, the method comprising:
 a. applying an operation based on a bioencryption format to decrypt a plurality of oligonucleotides encoding at least one item of information, wherein the operation comprises exposure of the plurality of oligonucleotides to one or more species;   b. enriching the plurality of oligonucleotides;   c. sequencing enriched oligonucleotides to generate nucleic acid sequences in a sequencing unit; and   d. converting, by a computing system, the nucleic acid sequences to at least one digital sequence, wherein the at least one digital sequence encodes for at least one item of information.   
     
     
         54 . A platform for retrieving information, the platform comprising:
 a. a material deposition system comprising a deposition unit for applying an operation based on a bioencryption format to decrypt a plurality of oligonucleotides encoding the at least one item of information, wherein the operation comprises exposure of the plurality of oligonucleotides to one or more species;   b. a sequencing unit for sequencing the plurality of oligonucleotides to obtain at least one nucleic acid sequence; and   c. a computing system comprising at least one processor and instructions executable by the at least one processor to perform operations comprising: converting the at least one nucleic acid sequence to at least one digital sequence, wherein the at least one digital sequence encodes for the at least one item of information.