KR20160001455A - DNA Memory for Data Storage - Google Patents

Abstract

The present invention relates to a method for storing and decoding data using DNA, and more particularly, to a method for storing and decoding data using DNA, comprising the steps of encoding a character into a base sequence, synthesizing an encoded base sequence to obtain a DNA, amplifying the obtained DNA, And a method of storing data using DNA. The present invention also relates to a method for decoding character-encoded DNA data comprising the steps of sequencing DNA in which the characters are stored by the above method and decoding the sequenced nucleotide sequence to obtain character data.
The DNA storage medium according to the present invention can play an important role as a next generation storage medium in a big data era because it can exceed data storage density which is a disadvantage of existing storage media and can store information stably even in a physical impact.

Description

[0001] The present invention relates to a DNA memory for data storage,

The present invention relates to a method for storing and decoding data using DNA, and more particularly, to a method for storing and decoding data using DNA, comprising the steps of encoding a character into a base sequence, synthesizing an encoded base sequence to obtain a DNA, amplifying the obtained DNA, And a method of storing data using DNA. The present invention also relates to a method for decoding character-encoded DNA data comprising the steps of sequencing DNA in which the characters are stored by the above method and decoding the sequenced nucleotide sequence to obtain character data.

By 2020, worldwide data volume is expected to reach 40 ZB, and since 2007, the amount of data produced worldwide has exceeded the storage capacity, requiring a new type of storage device. In the case of a magnetic tape widely used as a long-term recording medium, the data storage life is limited to about 10 years, and maintenance and management costs are continuously required. In the case of semiconductor storage devices, HDDs and SSDs are typical. In HDDs, they are very vulnerable to shocks and have a life span of 250,000 hours. Currently, 4TB is the maximum capacity. It is known that SSD is strong against impact, but its life is relatively shorter than HDD.

As an alternative technology capable of solving the data storage density limitations faced by existing information storage media, the DNA sequence has been considered as a storage medium capable of long-term storage of large capacity information and the possibility of a new technology to store large capacity data with recent DNA structures Respectively. DNA, as it is well known, is contained in the cell, the smallest unit of an organism, and contains all the genetic information. Depending on the information that DNA has, all organisms move as programmed. In humans, the DNA contained in a single cell is composed of 3 billion pairs of nucleotide sequences, and the capacity of about 1 TB is calculated if the size of the genetic information is all converted. One single cell contains two strands of DNA with a width of 2 nm and a length of 3 m. Therefore, theoretically, DNA, the next generation bio-storage capable of storing more than EB (10 ¹⁸ ), is very suitable as a biomaterial for storing information intensively. The shelf life is over 1,000 years and it seems to be easy to store at low cost.

In recent years, the amount of data generated explosively exceeds the capacity of a storage medium, causing an overload. As a result, attempts to develop a new storage medium continue to be made. Among them, the attempt to develop a new storage medium using DNA is very interesting. When DNA is used as a storage medium, it can exceed data storage density, which is a disadvantage of conventional storage media, and can store information stably even under physical impact.

On the other hand, attempts have been made to store video files in DNA (Nick Goldman, et al., Nature 494 (7435): 77-80, 2013). Specifically, a method of encoding digital data corresponding to 760 kilobytes, which is a part of a specific moving picture, into 5 to 6 digits by the Hoffman code method, and encoding each of the digits into a DNA base sequence is proposed. However, there is a disadvantage that the encoding of digital data to digits, the encoding of digits to DNA, and the encoding of DNA to DNA fragments are performed, which is relatively cumbersome.

As a result of intensive efforts to develop a storage medium using biomolecule DNA for development of an ultra-high-density storage, the present inventors have found that a method of encoding a DNA fragment in a single step, synthesizing and amplifying the encoded nucleotide sequence, DNA base sequence, and that the DNA base sequence can be decoded and restored to the original document, thereby completing the present invention.

An object of the present invention is to provide a method for storing character data using DNA.

Another object of the present invention is to provide a method of decrypting data of a character-encoded DNA by the above method.

In order to achieve the above object, the present invention provides a method for producing a polypeptide comprising: (a) encoding a letter into a base sequence consisting of A, T, G and C; (b) synthesizing a nucleotide sequence encoding a letter to obtain a character-encoded DNA; And (c) amplifying the obtained DNA and then inserting the amplified DNA into a vector.

The present invention also relates to a method for producing DNA comprising the steps of: (a) sequencing DNA in which a character is stored by the method; And (b) decoding the sequenced base sequence to obtain character data.

The DNA storage medium according to the present invention can play an important role as a next generation storage medium in a big data era because it can exceed data storage density which is a disadvantage of existing storage media and can store information stably even in a physical impact.

FIG. 1 illustrates a DNA memory or storage concept consisting of an encoding step, a synthesizing step, and a decoding step.
Fig. 2 shows a look-up table set up to encode document information into a DNA sequence.
FIG. 3 shows the Universal Declaration of Human Rights declared by the United Nations as text selected as an example of document information to be stored in the present invention.
Fig. 4 shows the contents of the Universal Declaration of Human Rights, which is the nucleotide sequence of the coated DNA according to the look-up table setting shown in Fig.
FIG. 5 shows the structure of a plasmid in which 22 DNA fragments (372 bp) encoded with encoded document information are inserted, and 14 bp DNAs of different base sequences are bound to both ends of a DNA fragment (372 bp) This means a sequence that specifies the sequence of 372 bp DNA fragments.
FIG. 6 shows a sequence of 44 (22 2) nucleotides consisting of 14 bp, each of which is a 14 bp terminal nucleotide sequence before and after 22 DNA nucleotides.

In the present invention, a storage medium capable of storing information with high storage densities using biomolecule DNA and stable to physical impacts was developed.

In the present invention, a specific character is encoded into a nucleotide sequence using Perl programming, and the encoded nucleotide sequence is synthesized using Ligase Chain Reaction (LCR). The obtained DNA was amplified and then inserted into a vector. As a result, the DNA in which the character data is stored can be confirmed.

Thus, in one aspect, the present invention provides a method of producing a polypeptide comprising: (a) encoding a letter with a nucleotide sequence consisting of A, T, G and C; (b) synthesizing a nucleotide sequence encoding a letter to obtain a character-encoded DNA; And (c) amplifying the obtained DNA and then inserting it into a vector.

In the present invention, the letters include various letters such as alphabets, Korean, Roman and Greek letters, and each letter can be represented by a specific nucleotide sequence having a length of 3 to 6 residues, more preferably 3 to 5 can be represented by a specific nucleotide sequence having a length of 4 residues, and most preferably can be represented by a specific nucleotide sequence having a length of 4 residues. Therefore, 27 (3 ³ ) to 46656 (6 ⁶ ) characters can be encoded as base sequences. The encoding of the characters into base sequences is programmed using the Look-Up Table.

In the present invention, a nucleotide sequence encoding a letter was synthesized by DNA using Ligase Chain Reaction (LCR) and amplified by PCR. In addition, the amplified DNA was inserted into a plasmid vector for stable storage.

In the present invention, PCR is the best known nucleic acid amplification method, and many modifications and applications thereof have been developed. For example, touchdown PCR, hot start PCR, nested PCR and booster PCR have been developed by modifying traditional PCR procedures to enhance the specificity or sensitivity of PCR. In addition, multiplex PCR, real-time PCR, differential display PCR (DD-PCR), rapid amplification of cDNA ends (RACE), inverse polymerase chain reaction chain reaction (IPCR), vectorette PCR and thermal asymmetric interlaced PCR (TAIL-PCR) have been developed for specific applications. For more information on PCR see McPherson, M.J., and Moller, S.G. PCR. BIOS Scientific Publishers, Springer-Verlag New York Berlin Heidelberg, N.Y. (2000), and the target nucleic acid molecule that can be used in the present invention preferably includes DNA.

In the present invention, a "vector" is a DNA storage means capable of stably storing a DNA fragment. For the purpose of the present invention, a plasmid vector is preferably used for stably storing a DNA fragment. A typical plasmid vector that can be used for this purpose has a structure comprising a restriction enzyme cleavage site into which a DNA fragment can be inserted. Even if an appropriate restriction enzyme cleavage site is not present, using a synthetic oligonucleotide adapter or a linker according to a conventional method can easily ligate the vector and the foreign DNA. Therefore, it may be stored in a vector until the DNA is decoded and stable memory preservation possible. In addition, in the case of DNA synthesized in the form of a fragment, it is troublesome to perform PCR by preparing a primer in order to produce an amplification product. However, when the synthesized DNA is stored in a vector, it can be transformed into an astronomical A number of plasmids can be obtained.

In the present invention, the nucleotide sequence of the DNA is sequenced so that the encoded DNA can be decoded, and the sequenced data is recovered as a character.

In the present invention, the nucleotide sequence encoding the character was analyzed using the Sanger's sequencing method, and the analyzed nucleotide sequence was decoded using a Perl program. As a result, It can be confirmed that the decoded characters match.

Accordingly, in another aspect, the present invention provides a method for detecting a DNA sequence comprising the steps of: (a) sequencing DNA in which a character is stored by the method; And (b) decoding the sequenced base sequence to obtain character data.

The characters of the present invention may include various characters such as alphabets, Korean, Roman and Greek characters, and the mapping from the base sequence to the characters is programmed using a reverse look-up table.

FIG. 1 generally shows a concept of a DNA memory or storage composed of the encoding step, the synthesizing step, and the decoding step.

In one aspect of the present invention, the content of the Universal Declaration of Human Rights is encoded into a nucleotide sequence using a DNA memory technology, and the DNA is synthesized and decoded from a nucleotide sequence to a character, so that the DNA memory is important as a next generation storage medium I can confirm that I can play a role.

Hereinafter, the present invention will be described in more detail with reference to Examples. It will be apparent to those skilled in the art that these embodiments are merely illustrative of the present invention and that the scope of the present invention is not limited to these embodiments.

However, in the present invention, only one embodiment is described in which one character is represented by four bases, but it will be apparent to those skilled in the art that encoding can be expressed by three, five, or six bases.

Example 1: Encoding step

Characters such as the English alphabet, special symbols and punctuation marks can be represented by a 4-mer, a specific base sequence of 4 residues in length (Fig. 2). The mapping from these characters to the 4-mer nucleotide sequence can be efficiently stored in the form of a forward hash, a variable type in the Perl programming language. I created a Perl program that performs encoding based on this hash variable. The encoding mode that is run in the Perl program can split English sentences into individual characters and then convert them into consecutive 4-mer sequences using forward hash variables.

As an example, the encoding was performed using the Universal Declaration of Human Rights text (Figure 3). First, save the text as a file named'original.txt 'in Notepad, and then open the Windows Command Prompt (CMD) in the folder where the file is saved. Enter "C: \ Users \ Hwang \ Desktop \ Moonil_Kim \ 2014.04.23." String_converter.exe example1_original.txt example1_encoded.txt encode "in the command window and press enter to create an encoded file (example1_encoded.txt). Fig. 4 shows the contents of the Universal Declaration of Human Rights document as an encoded base sequence.

Example 2 DNA Sequence Synthesis and Cloning

The text of the Universal Declaration of Human Rights, produced by the Look-Up Table, can be represented by a total of 8,184 bp sequence and is divided into a total of 22 400 bp (14 bp + 372 bp + 14 bp) Among the 400 bp DNA fragment, the encoded DNA fragment is a fragment of 372 bp in length, and the 14 bp fragment bound to both ends of the 400 bp DNA fragment is a nucleotide sequence specifying the sequence of the 372 bp DNA fragment (FIG. 5). A fragment of 14 bp, each of which is bonded before and after the 22 DNA base sequences, that is, the base sequence is shown in Fig.

Twenty-two 400 bp DNA fragments were synthesized by the phosphite triester method using a small fragment of oligo (about 20-50 bp), assembled into Ligase Chain Reaction (LCR), and finally the desired 400 bp fragment was obtained And then amplified by PCR. PCR conditions were denaturation (96 min for 1 min), annealing (1 min) using Mastercycler gradient PCR (Ependorf), 1 l of template DNA (10 pmol), 1 l of each primer, 4 l of primix , 1 minute at 52.5) and elongation (72 minutes at 2 minutes).

The amplified PCR product was purified by Plasmid mini-prep kit (Solgent), and 70% ethanol was added to precipitate DNA. The recovered DNA was confirmed by agarose gel electrophoresis. The cutting the purified DNA with restriction enzymes Sal BanH and, connecting with a plasmid pET32a T4 DNA ligase (Takara) to (Novagen) digested with the same restriction enzymes Sal BanH and with the following, this E. coli XL -1-Blue, and the DNA was inserted into the plasmid vector.

Example 3: Decoding step

The DNA sequencing step was performed with Sanger's sequencing method. In Example 1, the DNA encoding the letter was subjected to PCR using an oligonucleotide composed of 15 to 20 bases and Taq polymerase. The amplified product was electrophoresed with agarose gel, purified with AccuPrep ^™ gel purification kit, followed by Sanger sequencing, and sequencing data was analyzed using Lasergene (DNAstar, Madison, Wis.). The nucleotide sequence obtained by DNA sequencing was decoded by a character using a Perl program.

The decoding mode operated in Perl program is to remove the adapter sequence from the sequence obtained by sequencing, then read it by 4 residues, convert it to a character using reverse hash, Respectively.

As a result, the decoded file (example1_decoded.txt) was confirmed to match the original file using a utility called WinMerge.

While the present invention has been particularly shown and described with reference to specific embodiments thereof, those skilled in the art will appreciate that such specific embodiments are merely preferred embodiments and that the scope of the present invention is not limited thereby. something to do. It is therefore intended that the scope of the invention be defined by the claims appended hereto and their equivalents.

Claims (8)

A method for storing data using DNA comprising the steps of:
(a) encoding a letter with a nucleotide sequence consisting of A, T, G and C;
(b) synthesizing a nucleotide sequence encoding a letter to obtain a character-encoded DNA; And
(c) amplifying the obtained DNA and then inserting it into a vector.
The method of claim 1, wherein the characters are selected from the group consisting of alphabets, Korean, hiragana, katakana, roman, greek, hebrew, Cyrillic, Bengali, Gujarati, Olchiki, Lao, Tamil, Telugu, , Tibetan letters, Myanmar letters, Arabic letters, Armenian letters, Coptic letters, Cherokee letters, special characters, punctuation marks, symbols and numbers.
2. The method of claim 1, wherein each of the characters is encoded by encoding from 3 to 6 specific nucleotide sequences.
2. The method of claim 1, wherein the encoding is based on a look-up table in which a base sequence is mapped from a character.
The method according to claim 1, wherein the DNA synthesis is performed using an oligo fragment and a ligase chain reaction (LCR).
A method for decrypting character-encoded DNA data comprising the steps of:
(a) sequencing DNA in which a character is stored by the method of claim 1; And
(d) decoding the sequenced base sequence to obtain character data.
7. The method of claim 6, wherein the characters are alphabets, Korean, Hiragana, Katakana, Roman, Greek, Hebrew, Cyrillic, Bengali, Gujarati, Olchiki, Lao, Tamil, Telugu, , Tibetan letters, Myanmar letters, Arabic letters, Armenian letters, Coptic letters, Cherokee letters, special characters, punctuation marks, symbols and numbers.
7. The method of claim 6, wherein the decoding is based on a look-up table in which characters are mapped from a base sequence.

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