Nucleic acid based data storage using enzymatic bioencryption

1. A method for storing information, the method comprising:

a) receiving, by a computing system, at least one item of information in a form of at least one digital sequence;

b) receiving, by the computing system, instructions for enzymatic bioencryption;

c) converting, by the computing system, the at least one digital sequence to digital sequences of a plurality of oligonucleotides based on the instructions, wherein the digital sequences of the plurality of oligonucleotides are configured for decryption by exposure of the plurality of oligonucleotides to a nuclease complex;

d) synthesizing the plurality of oligonucleotides in a synthesizer; and

e) storing the plurality of oligonucleotides.

2. The method of claim 1 , wherein the enzymatic bioencryption comprises CRISPR/Cas-based bioencryption.

3. The method of claim 1 , wherein the nuclease complex comprises an enzyme as set out in Table 1:

Recognition Sequence

Enzyme

AA/CGTT

AclI

A/AGCTT

HindIII

HindII sold under the

trademark HindIII-HF®

AAT/ATT

SspI

SspI sold under the

trademark SspI-HF®

/AATT

MluCI

Tsp509I

A/CATGT

PciI

A/CCGGT

AgeI

AgeI sold under the

trademark AgeI-HF®

ACCTGC(4/8)

BspMI

BfuAI

A/CCWGGT

SexAI

A/CGCGT

MluI

MluI sold under the

trademark MluI-HF®

ACGGC(12/14)

BceAI

A/CGT

HpvCH4IV

ACN/GT

HpvCH4III

(10/15)ACNNNNGTAYC(12/7) 

BaeI

(SEQ ID NO: 5)

(9/12)ACNNNNNCTCC(10/7) 

BsaXI

(SEQ ID NO: 6)

A/CRYGT

AflIII

A/CTAGT

SpeI

SpeI sold under the

trademark SpeI-HF®

ACTGG(1/-1)

BsrI

ACTGGG(5/4)

BmrI

A/GATCT

BgIII

AGC/GCT

AfeI

AG/CT

AluI

AGG/CCT

StuI

AGT/ACT

ScaI

ScaI sold under the

trademark ScaI-HF®

AT/CGAT

ClaI

BspDI

ATCTATGTCGGGTGCGGAGAAAGAGG

PI-SceI

TAAT(-15/-19)

(SEQ ID NO: 7)

ATGCA/T

NsiI

NsiI sold under the

trademark NsiI-HF®

AT/TAAT

AseI

ATTT/AAAT

SwaI

(11/13)CAANNNNNGTGG(12/10) 

CspCI

(SEQ ID NO: 8)

C/AATTG

MfeI

MfeI sold under the

trademark MfeI-HF®

CACGAG(-5/-1)

BssSI

BssSαI

CACGAG

Nb.BssSI

CACGTC(-3/-3)

BmgBI

CAC/GTG

PmlI

CACNNN/GTG

DraIII

DraIII sold under the

trademark DraIII-HF®

CACNN/NNGTG 

AleI

(SEQ ID NO: 9)

CAGCAG(25/27)

EcoP15I

CAG/CTG

PvuII

PvuII sold under the

trademark PvuII-HF®

CAGNNN/CTG

AlwNI

CAGTG(2/0)

BtsIMutI

NNCASTGNN/

TSpRI

CA/TATG

NdeI

CATG/

NlaIII

C/ATG

CviAII

/CATG

FatI

CAYNN/NNRTG 

MslI

(SEQ ID NO: 10)

CC(12/16)

FspEI

CCANNNNN/NNNNTGG

XcmI

(SEQ ID NO: 11)

CCANNNNN/NTGG 

BstXI

(SEQ ID NO: 12)

CCANNNN/NTGG 

PfIMI

(SEQ ID NO: 13)

CCATC(4/5)

BccI

C/CATGG

NcoI

NcoI sold under the

trademark NcoI-HF®

CCCAGC(-5/-l)

BseYI

CCCGC(4/6)

FauI

CCC/GGG

SmaI

C/CCGGG

XmaI

TspMI

(0/-1)CCD

Nt.CviPII

CCDG(10/14)

LpnPI

CCGC(-3/-l)

AciI

CCGC/GG

SacII

CCGCTC(-3/-3)

BsrBI

C/CGG

MspI

HpaII

CC/NGG

ScrFI

/CCNGG

BssKI

StvD4I

C/CNNGG

BsaJI

CCNNNNN/NNGG 

BslI

(SEQ ID NO: 14)

C/CRYGG

BtgI

CC/SGG

NciI

C/CTAGG

AvrII

CCTC(7/6)

MnlI

CCTCAGC(-5/-2)

BbvCI

CCTCAGC

Nb.BbvCI

CCTCAGC(-5/-7)

Nt.BbvCI

CCTGCA/GG

SbfI

SbfI sold under the

trademark SbfI-HF®

CCTNAGC(-5/-2)

Bpu10I

CC/TNAGG

Bsu361

CCTNN/NNNAGG 

EcoNI

(SEQ ID NO: 15)

CCTTC(6/5)

HpyAV

CC/WGG

BstNI

/CCWGG

PsoGI

C/CWWGG

StyI

StyI sold under the

trademark StyI-HF®

(10/12)CGANNNNNNTGC(12/10) 

BcgI

(SEQ ID NO: 16)

CGAT/CG

PvuI

PvuI sold under the

trademark PvuI-HF®

CG/CG

BstUI

C/GGCCG

EagI

EagI sold under the

trademark EagI-HF®

CG/GWCCG

RsrII

CGRY/CG

BsiEI

C/GTACG

BsiWI

BsiWI sold under the

trademark BsiWI-HF®

CGTCTC(l/5)

BsmBI

CGWCG/

Hdv99I

CMG/CKG

MspAlI

CNNR(9/13)

MspJI

CR/CCGGYG

SgrAI

C/TAG

BfaI

CTCAG(9/7)

BsdCNI

C/TCGAG

XhoI

PaeR7I

TliI

CTCTTC(l/4)

EarI

CTGAAG(16/14)

AcuI

CTGCA/G

PstI

PstI sold under the

trademark PstI-HF®

CTGGAG(16/14)

BpmI

C/TNAG

DdeI

C/TRYAG

SfcI

C/TTAAG

AflII

CTTGAG(16/14)

BpuEI

C/TYRAG

SmlI

C/YCGRG

AvaI

BsoBI

GAAGA(8/7)

MboII

GAAGAC(2/6)

BbsI

BbsI sold under the

trademark BbsI-HF®

GAANN/NNTTC 

XmnI

(SEQ ID NO: 17)

GAATGC(1/-1)

BsmI

GAATGC

Nb.BsmI

G/AATTC

EcoRI

EcoRI sold under the

trademark EcoRI-HF®

GACGC(5/10)

HgaI

GACGT/C

AatII

GAC/GTC

ZraI

GACN/NNGTC

Tth111I

PflFI

GACNN/NNGTC 

PshAI

(SEQ ID NO: 18)

GACNNN/NNGTC 

AhdI

(SEQ ID NO: 19)

GACNNNN/NNGTC 

DrdI

(SEQ ID NO: 20)

GAG/CTC

Eco53kI

GAGCT/C

SacI

SacI sold under the

trademark SacI-HF®

GAGGAG(10/8)

BseRI

GAGTC(4/5)

PleI

GAGTC(4/-5)

Nt.BstNBI

GAGTC(5/5)

MlyI

G/ANTC

HinfI

GAT/ATC

EcoRV

EcoRV sold under the

trademark EcoRV-HF®

/GATC

MboI

Sau3AI

DpnII

BfuCI

GA/TC

DpnI

GATNN/NNATC 

BsaBI

(SEQ ID NO: 21)

G/AWTC

TfiI

GCAATG(2/0)

BsrDI

GCAATG

Nb.BsrDI

GCAGC(8/12)

BbvI

GCAGTG(2/0)

BtsI

Btsαl

GCAGTG

Nb.BtsI

GCANNNN/NTGC 

BstAPI

(SEQ ID NO: 22)

GCATC(5/9)

SfaNI

GCATG/C

SphI

SphI sold under the

trademark SphI-HF®

GCCC/GGGC

SrfI

GCCGAG(21/19)

NmeAIII

GCC/GGC

NaeI

G/CCGGC

NgoMIV

GCCNNNN/NGGC 

BglI

(SEQ ID NO: 23)

GCGAT/CGC

AsiSI

GCGATG(10/14)

BtgZI

G/CGC

HinP1I

GCG/C

HhaI

G/CGCGC

BssHII

GC/GGCCGC

NotI

NotI sold under the

trademark NotI-HF®

GC/NGC

Fnu4HI

GCN/NGC

Cac8I

GCNNNNN/NNGC 

MwoI

(SEQ ID NO: 24)

G/CTAGC

NheI

NheI sold under the

trademark NheI-HF®

GCTAG/C

BmtI

BmtI sold under the

trademark BmtI-HF®

GCTCTTC(l/4)

SapI

BspQI

GCTCTTC(l/-7)

Nt.BspQI

GC/TNAGC

BlpI

G/CWGC

TseI

ApeKI

GDGCH/C

Bspl286I

GGATC(4/5)

AlwI

GGATC(4/-5)

Nt.AlwI

G/GATCC

BamHI

BamHI sold under the

trademark BamHI-HF®

GGATG(9/13)

FokI

GGATG(2/0)

BtsCI

GG/CC

HaeIII

PhoI

GGCCGG/CC

FseI

GGCCNNNN/NGGCC 

SfiI

(SEQ ID NO: 25)

GG/CGCC

NarI

G/GCGCC

KasI

GGC/GCC

SfoI

GGCGC/C

PluTI

GG/CGCGCC

AscI

GGCGGA(11/9)

EciI

GGGAC(10/14)

BsmFI

GGGCC/C

ApaI

G/GGCCC

PspOMI

G/GNCC

Sau96I

GGN/NCC

NlaIV

GGTAC/C

KpnI

KpnI sold under the

trademark KpnI-HF®

G/GTACC

Acc65I

GGTCTC(1/5)

BsaI

BsaI sold under the

trademark BsaI-HF®

GGTGA(8/7)

HphI

G/GTNACC

BstEII

BstEII sold under the

trademark BstEII-HF®

G/GWCC

AvaII

G/GYRCC

BanI

GKGCM/C

BaeGI

GR/CGYC

BsaHI

GRGCY/C

BanII

GT/AC

RsaI

G/TAC

CviQI

GTA/TAC

BstZ17I

BstZ17I sold under the

trademark BstZ17I-HF®

GTATCC(6/5)

BciVI

G/TCGAC

SalI

SalI sold under the

trademark SalI-HF®

GTCTC(1/-5)

Nt.BsmAI

GTCTC(1/5)

BsmAI

BcoDI

G/TGCAC

ApaLI

GTGCAG(16/14)

BsgI

GT/MKAC

AccI

GTN/NAC

Hpy166II

/GTSAC

Tsp45I

GTT/AAC

HpaI

GTTT/AAAC

PmeI

GTY/RAC

HincII

GWGCW/C

BsiHKAI

R/AATTY

ApoI

ApoI-HF

RCATG/Y

NspI

R/CCGGY

BsrFI

BsrFαI

R/GATCY

BstYI

RGCGC/Y

HaeII

RG/CY

CviKI-1

RG/GNCCY

EcoO109I

RG/GWCCY

PpuMI

TAACTATAACGGTCCTAAGGTAGCGAA 

I-CeuI

(-9/-13)

(SEQ ID NO: 26)

TAC/GTA

SnaBI

TAGGGATAACAGGGTAAT(9/-13) 

I-SceI

(SEQ ID NO: 27)

T/CATGA

BSpHI

T/CCGGA

BspEI

TCCRAC(20/18)

MmeI

T/CGA

TaqαI

TCG/CGA

NruI

NruI sold under the

trademark NruI-HF®

TCN/GA

Hpyl88I

TC/NNGA

Hpyl88III

T/CTAGA

XbaI

T/GATCA

BclI

TG/CA

HpvCH4V

TGC/GCA

FspI

TGGCAAACAGCTATTATGGGTATTA

PI-PspI

TGGGT(-13/-17)

(SEQ ID NO: 28)

TGG/CCA

MscI

T/GTACA

BsrGI

BsrGI sold under the

trademark BsrGI-HF®

T/TAA

MseI

TTAAT/TAA

PacI

TTA/TAA

PsiI

TT/CGAA

BstBI

TTT/AAA

DraI

VC/TCGAGB

PspXI

W/CCGGW

BsaWI

YAC/GTR

BsaAI

Y/GGCCR

EaeI

4. The method of claim 1 , wherein the plurality of oligonucleotides comprises at least 100,000 oligonucleotides.

5. The method of claim 1 , wherein the plurality of oligonucleotides comprises at least 10 billion oligonucleotides.

6. A platform for storing information, the platform comprising:

a) a computing system comprising at least one processor and instructions executable by the at least one processor to perform operations comprising:

i) receiving at least one item of information in a form of at least one digital sequence;

ii) receiving instructions for enzymatic bioencryption; and

iii) converting the at least one digital sequence to digital sequences of a plurality of oligonucleotides based on the instructions, wherein the digital sequences of the plurality of oligonucleotides are configured for decryption by exposure of the plurality of oligonucleotides to a nuclease complex; and

b) a material deposition system for deposition and storage of oligonucleotides comprising:

i) a synthesizer for receiving instructions from the computing system for synthesizing the plurality of oligonucleotides,

wherein the synthesizer comprises a substrate for storing the plurality of oligonucleotides.

7. The method of claim 1 , wherein the decryption comprises contacting the plurality of oligonucleotides with Cas nuclease (CRISPR-associated nuclease), a Zinc Finger Nuclease (ZFN), a Transcription Activator-Like Effector Nuclease, an Argonaute nuclease, Si Nuclease, a mung bean nuclease, or a DNAse.

8. The method of claim 1 , wherein the method further comprises sequencing the plurality of oligonucleotides.

9. The method of claim 1 , wherein the plurality of oligonucleotides is stored ex-vivo.

10. The method of claim 1 , wherein synthesizing the plurality of oligonucleotides comprises phosphoramidite chemical synthesis.

11. The method of claim 1 , wherein the at least one digital sequence comprises at least 1 MB.

12. The platform of claim 6 , wherein the decryption comprises contacting the plurality of oligonucleotides with Cas nuclease (CRISPR associated), a Zinc Finger Nuclease (ZFN), a Transcription Activator-Like Effector Nuclease, an Argonaute nuclease, Si Nuclease, a mung bean nuclease, or a DNAse.

13. The platform of claim 6 , wherein the computing system comprises a distributed computing system.