Array dot type DNA information storage method and application

Abstract

The invention discloses an array dot type DNA information storage method and application. The array point type DNA information storage method comprises the following steps: firstly, converting to-be-stored information into a binary sequence by using a coding algorithm, and converting the binary sequence into a base sequence according to a preset mapping relation; then preparing DNA ink containing the base sequence, transferring the DNA ink to the edge of a substrate material, moving a flexible platform to enable a probe to be in contact with the DNA ink, then dropping the probe at a first preset position of the substrate material and lifting the probe to obtain the DNA nanodot containing the to-be-stored information so as to realize DNA information storage. By adopting the DNA information storage method, the accuracy of DNA information reading and the read-write rate of DNA storage can be improved, and the DNA information storage method is good in safety and has a relatively good application prospect.

Description

Technical Field

[0001] This invention relates to the field of bioinformatics technology, and in particular to a method and application of array-based DNA information storage. Background Technology

[0002] DNA information storage is a novel data storage technology that utilizes deoxyribonucleic acid (DNA) molecules as a medium. Currently, most DNA information storage methods involve synthesizing DNA strands to store information. The basic workflow includes five steps: encoding, writing, storage, reading, and decoding. First, the information to be stored is encoded and converted into a DNA sequence. Next, the information is written by synthesizing the corresponding DNA strand. The DNA strand is then preserved in forms such as solutions, dry powders, microspheres, or implanted into organisms. When this information needs to be read, sequencing technology is used to obtain the DNA strand's sequence information. Finally, decoding is performed to reconstruct the original information. DNA information storage methods can achieve ultra-high-density information storage and, under relatively stable conditions, have an extremely long storage lifespan.

[0003] In related technologies, DNA information writing is mainly performed through DNA synthesis, while information retrieval is mainly performed through DNA sequencing. Besides the basic cost of bases, other costs such as operation and maintenance, reagents and consumables, quality control, and labor contribute to the current high cost of DNA information storage. Studies show that the average cost of synthesizing DNA is approximately $10-3 per base; synthesizing 2 MB of DNA data requires $7,000, while retrieving data requires $2,000, thus resulting in high storage costs. Secondly, the DNA synthesis process is often accompanied by a high error rate. Due to factors such as insufficient capping, insufficient purity of reaction reagents, excessively high humidity in the reaction environment, excessively long acid treatment time, and insufficient coupling time, various errors such as base deletions and mutations can occur during DNA synthesis. The error rate of conventional DNA synthesis is around 0.1-0.3%, while the error rate is even higher in the assembly and synthesis of large DNA fragments. Furthermore, long DNA sequences may interact internally, causing folding and resulting in base sequence disorder. During sequencing, PCR amplification has a certain bias and mismatch rate, which affects the coverage and sequencing accuracy of the final library. Therefore, the accuracy of DNA storage is also low. DNA synthesis involves the use of numerous toxic chemical reagents and produces toxic byproducts, which contradicts the principles of green and sustainable development. Furthermore, it is worth noting that the processes of DNA synthesis and sequencing result in a significant problem with current DNA information storage technologies: slow read and write speeds.

[0004] Therefore, there is an urgent need to find a DNA information storage method that can help improve the accuracy of DNA information reading and the read / write speed of DNA storage, while also ensuring good security. Summary of the Invention

[0005] The first objective of this invention is to provide an array-based DNA information storage method.

[0006] The second objective of this invention is to provide a method for reading information stored in array-type DNA.

[0007] A third aspect of the present invention is to provide a storage system.

[0008] The fourth aspect of this invention aims to provide the application of a method for storing array-dot DNA information or a method for reading array-dot DNA stored information in DNA data storage.

[0009] To achieve the above objectives, the technical solution adopted by the present invention is as follows: A first aspect of the present invention provides a method for storing array-type DNA information, comprising the following steps: S1. The information to be stored is converted into a binary sequence using an encoding algorithm, and the binary sequence is converted into a base sequence according to a preset mapping relationship; S2. Prepare DNA ink containing the base sequence, then transfer it to the edge of the substrate material, move the flexible platform to make the probe contact the DNA ink, and then drop the probe at the first preset position on the substrate material and lift the probe to obtain DNA nanodots containing the information to be stored, thereby realizing DNA information storage.

[0010] In some embodiments of the present invention, the information to be stored includes at least one of images, text, programs, audio, and video.

[0011] In some embodiments of the present invention, the concentration of the DNA ink is 10-100 µM.

[0012] In some embodiments of the present invention, the solvent of the DNA ink is selected from water, phosphate buffer, or physiological saline.

[0013] In some embodiments of the present invention, the volume of the DNA ink transfer is 10-1000 µL.

[0014] In some embodiments of the present invention, the DNA ink transfer is performed using at least one of a syringe, a pipette, and a dropper.

[0015] In some embodiments of the present invention, the substrate material is selected from any one of mica sheets, polished silicon wafers, glass sheets, or graphite.

[0016] In some embodiments of the present invention, the distance between the edge of the substrate material and the substrate material is 0-1000 µm.

[0017] In some embodiments of the present invention, the substrate material is scanned using an atomic force microscope before the probe contacts the DNA ink.

[0018] In some embodiments of the present invention, the scanning range is 1-10000 µm. 2 .

[0019] In some embodiments of the present invention, the roughness of the substrate material is ≤5 nm. For example, it can be 5, 4, 3, 2, 1, 0.5, or 0.1 nm, etc.

[0020] In some embodiments of the present invention, the flexible platform has a movement range of 10-1000 µm.

[0021] In some embodiments of the present invention, the probe contacts the DNA ink for 1-50 seconds. For example, it can be 1, 50, 10, 20, 30, 40, or 50 seconds.

[0022] In some embodiments of the present invention, the time for the needle to fall at the first preset position is 10-100 seconds. For example, it can be 10, 20, 30, 50, 80, or 100 seconds.

[0023] In some embodiments of the present invention, the needle is allowed to rest for 10-50 seconds before dropping at the first preset position. This resting period helps to improve stability and accuracy.

[0024] In some embodiments of the present invention, after obtaining the DNA nanodots containing the information to be stored, the process further includes washing the needle. And / or, by replacing the DNA ink and the first preset position, repeat step S2 to prepare the second DNA nanodot.

[0025] In a second aspect, the present invention provides a method for reading array-dotted DNA storage information, which uses a base pairing force curve or a hybridization colorimetric method to identify bases in the array-dotted DNA storage information obtained by the array-dotted DNA information storage method described in the first aspect, and then reads the information according to the preset mapping relationship.

[0026] A third aspect of the invention provides a storage system comprising a storage unit and a reading unit, wherein the storage unit operates the array-dot DNA information storage method as described in the first aspect.

[0027] A fourth aspect of the present invention provides the application of the array-dot DNA information storage method as described in the first aspect or the array-dot DNA storage information reading method as described in the second aspect in DNA data storage.

[0028] The array-dot DNA information storage method of the present invention has at least the following beneficial effects: the DNA information storage method of the present invention helps to improve the accuracy of DNA information reading and the read / write speed of DNA storage, and has good security and good application prospects.

[0029] Other features and advantages of the present invention will be set forth in the following description. Attached Figure Description

[0030] The present invention will be further described below with reference to the accompanying drawings and embodiments, wherein: Figure 1 This is a schematic diagram of the array-type DNA information storage process of the present invention.

[0031] Figure 2 This is a schematic diagram of the DNA nanodot writing process of the present invention.

[0032] Figure 3 These are AFM scan images of the four types of DNA nanodots of this invention.

[0033] Figure 4 This is a schematic diagram illustrating the reading of DNA nanodots according to the present invention.

[0034] Figure 5 This is a schematic diagram illustrating the encoding, writing, reading, and decoding processes using array-based DNA information storage technology in this invention. Detailed Implementation

[0035] The following will describe the concept and technical effects of the present invention clearly and completely with reference to embodiments, so as to fully understand the purpose, features and effects of the present invention. Obviously, the described embodiments are only some embodiments of the present invention, not all embodiments. Other embodiments obtained by those skilled in the art based on the embodiments of the present invention without creative effort are all within the scope of protection of the present invention.

[0036] The terms "preferred," "more preferably," etc., used in this invention refer to embodiments of the invention that provide certain beneficial effects under certain circumstances. However, other embodiments may also be preferred under the same or other circumstances. Furthermore, the description of one or more preferred embodiments does not imply that other embodiments are unavailable, nor is it intended to exclude other embodiments from the scope of this invention.

[0037] When a numerical range is disclosed herein, the range is considered continuous and includes the minimum and maximum values ​​of the range, as well as every value between the minimum and maximum values. Furthermore, when the range refers to integers, it includes every integer between the minimum and maximum values ​​of the range. Additionally, when multiple ranges are provided to describe a feature or characteristic, the ranges may be combined. In other words, unless otherwise specified, all ranges disclosed herein should be understood to include any and all subranges to which they are incorporated.

[0038] In the description of this invention, the reference term "and / or" includes all and any combination of one or more of the associated listed items.

[0039] In the description of this invention, the terms "one embodiment," "some embodiments," "illustrative embodiment," "example," "specific example," or "some examples," etc., refer to specific features, structures, materials, or characteristics described in connection with that embodiment or example, which are included in at least one embodiment or example of the invention. In this specification, the illustrative expressions of the above terms do not necessarily refer to the same embodiment or example. Furthermore, the specific features, structures, materials, or characteristics described may be combined in any suitable manner in one or more embodiments or examples.

[0040] Unless otherwise specified in the examples, the procedures should be performed under standard conditions or conditions recommended by the manufacturer. Reagents or instruments whose manufacturers are not specified are all commercially available products.

[0041] refer to Figure 1 The diagram illustrates the process of array-based DNA information storage, with key steps including encoding, writing, reading, and decoding.

[0042] This invention provides a method for storing array-based DNA information, comprising: S1. Use an encoding algorithm to convert the information to be stored into a binary sequence, and convert the binary sequence into a base sequence according to a preset mapping relationship; S2. A strategy combining atomic force microscopy (AFM) and a flexible nanoplatform was adopted to write DNA nanodots.

[0043] In some specific implementations, the information to be stored may include one or more of the data information that can exist on the computer, such as images, text, programs, audio, and video.

[0044] In some specific implementations, when obtaining the binary sequence corresponding to the information to be stored, the encoding information corresponding to the information to be stored can be obtained, and the corresponding encoding information can be converted into binary encoding information to obtain the corresponding binary sequence. For example, the text in the text information can be converted into the corresponding ASCII (American Standard Code for Information Interchange) encoding or UNICODE (Universal Character Set) encoding, and then the encoding information can be converted into a binary sequence.

[0045] In some specific embodiments, the binary sequence is converted into a base sequence according to a preset mapping relationship. Since the bases in DNA include four types of natural bases: adenine (A), guanine (G), cytosine (C), and thymine (T), the preset mapping relationship can be a binary-to-quaternary mapping relationship.

[0046] In some specific implementations, the mapping relationship can be: 00 maps to A, 01 maps to T, 11 maps to C, and 10 maps to G. This mapping relationship can also be a combination of different binary codes and base codes, for example, 11 maps to A, 10 maps to T, 01 maps to C, and 00 maps to G.

[0047] In some specific embodiments, the bases in the base sequence may also be non-natural bases. Non-natural bases refer to optional bases or base analogues other than the four bases A, G, C, and T mentioned above. Examples of non-natural bases include at least one of the following: methylcytosine (mC), methyladenine (mA), methylguanine (mG), methylthymidine (mT), hydroxymethylcytosine (hmC), carboxycytosine (caC), formylcytosine (fC), isocytosine (isoC), inosine (I), nitroindole, nitropyrrole, artificial base Z, artificial base P, artificial base S, and artificial base B. Non-natural bases also include at least one of the following: m6A, m5C, hm5C, f5C, ca5C, 4-nitroindole, 5-nitroindole, 6-nitroindole, and 3-nitropyrrole.

[0048] In some specific embodiments, step S1 includes: converting the information to be stored into binary "0, 1" codes, and then writing the binary "0, 1" codes into quaternary "adenine (A), guanine (G), thymine (T), cytosine (C)" codes.

[0049] refer to Figure 2 As shown, this invention employs a strategy combining AFM and a flexible nanoplatform to achieve DNA nanodot writing, specifically including: S11. Dissolve the base sequence to be written (such as DNA powder) in a solvent to prepare DNA ink; S12. Transfer the DNA ink to the edge of the substrate material, move the nano-flexible platform to allow the atomic force microscope probe to pick up the DNA ink, and then move it to the needle placement position (marked as the origin, coordinates 0, 0). After placing the needle on the substrate material, lift the needle to complete the writing of a DNA nanodot containing stored information. S13. Repeat step S12, changing the base sequence to be written and the pin position (coordinates X, Y), thereby realizing information writing.

[0050] In some specific implementations, the base sequence to be written can be natural DNA or artificially synthesized DNA.

[0051] In some specific embodiments, the solvent is selected from at least one of water, phosphate buffer, or physiological saline. Ultrapure water is preferred.

[0052] In some specific embodiments, the concentration of the DNA ink is 10~100 µM.

[0053] In some specific embodiments, the substrate material can be a mica sheet, a polished silicon wafer, a glass sheet, or graphite, etc. Mica sheets are preferred.

[0054] In some specific embodiments, when the DNA ink is transferred to the edge of the substrate material, 10 to 1000 µL of DNA ink is transferred at a distance of 0 to 1000 µm from the substrate material.

[0055] Specifically, when transferring DNA ink to the edge of the substrate material, syringes, pipettes, or droppers can be used.

[0056] In some specific embodiments, the method further includes scanning the surface of the substrate material in contact mode using an atomic force microscope before using an atomic force microscope probe to pick up DNA ink.

[0057] Specifically, the scanning range is 1-10000 µm. 2 If the roughness is ≤5 nm, proceed to the subsequent DNA ink application step. Excessive roughness will interfere with the recognition of the DNA nanoarray.

[0058] In some specific implementations, the atomic force microscope probe dips into the DNA ink in a contact mode.

[0059] In some specific embodiments, in S12, when the moving flexible platform causes the AFM probe to pick up DNA ink in contact mode, the time for the AFM probe to pick up DNA ink is 1-50 s. For example, it can be 10, 15, 20, 25, 30, 40, or 50 s, etc.

[0060] In some specific embodiments, in S12, after the flexible platform moves to allow the AFM probe to pick up DNA ink in contact mode, the movement range of the flexible platform is 10~1000 µm. For example, it can be 10, 20, 50, 80, 100, 150, 200, 400, 600, 800 or 1000 µm, etc.

[0061] In some specific implementations, the writing of a DNA nanodot containing stored information is followed by needle washing.

[0062] Specifically, the needle washing process includes: using a syringe to transfer ultrapure water to the edge of a mica sheet, then moving a flexible platform to allow the probe to pick up the ultrapure water, and then moving the flexible platform again to return the probe to its initial position, thus completing one needle washing process.

[0063] In some specific embodiments, during S13, when changing the needle position (coordinates X, Y), the value of X ranges from -1000 to 1000 µm, and the value of Y ranges from -1000 to 1000 µm. In some specific embodiments, the array-dot DNA information storage method specifically includes the following steps: S21. Using a specific encoding method, the binary "0, 1" codes are written into quaternary "A, G, T, C" codes, and DNA dry powder is prepared. S22. Dissolve the DNA powder in ultrapure water to prepare DNA ink with a concentration in the range of 10-100 µM, and use a syringe to transfer the DNA ink to the edge of the mica sheet. S23. Scan the surface of the mica sheet with AFM. If the roughness is ≤5 nm, proceed to the next step. S24. Move the flexible platform to dip the probe into the DNA ink, and then move the flexible platform again to return the probe to the position where the horizontal coordinate (X) is 0 and the vertical coordinate (Y) is 0. After the system stabilizes, place the probe at this position to deliver the DNA ink to the substrate surface and complete the writing of a DNA nanodot. S25. Change the x-coordinate X and y-coordinate Y values ​​of the target needle placement position. The value of X ranges from -1000 to 1000 µm, and the value of Y ranges from -1000 to 1000 µm. Repeat the previous step to write a series of DNA nanodots.

[0064] refer to Figure 3As shown, in some specific embodiments, different types of DNA nanodots can be written by repeating steps S22 to S25 after preparing different types of DNA inks.

[0065] refer to Figure 4 As shown, the present invention provides a method for reading array-dot DNA information, including: The mobile flexible platform allows the probe to be dipped in DNA ink. When the probe is brought close to the DNA nanodots on the substrate, the corresponding base pairing force curve can be obtained. Base identification is then performed using the base pairing force curve. The identified "A, G, T, C" codes are then converted into binary "0, 1" codes.

[0066] In some specific implementations, the method for reading array-dot DNA information also includes using DNA strand hybridization colorimetry or Raman detection methods.

[0067] Example 1: This embodiment provides a method and application for array-based DNA information storage, specifically including the following: 1. Encoding: Encoding is performed using a "simple mapping" method, specifically: 00 is mapped to A, 10 to T, 01 to G, and 11 to C. For example... Figure 5 As shown, using the above encoding method, the binary "0010" can be written as the quaternary "AT".

[0068] 2. Write: To facilitate the detection of various DNA sequences, homopolymers can be used instead of individual nucleotides; for example, a short DNA chain with the sequence "AAAAAA" can replace "A," and a short DNA chain with the sequence "TTTTTT" can replace "T." The aforementioned DNA powders were dissolved in ultrapure water to prepare DNA inks with a concentration of 25 µM. The mica sheet surface was scanned using AFM in contact mode, with a scanning range of 100 µm. 2 The roughness is 2 nm, which meets the requirements for the flatness of the substrate material.

[0069] Specifically, first use a syringe to transfer "AAAAAA" ink to the edge of the mica sheet, then move the flexible platform to make the probe dip into "AAAAAA" ink, move the flexible platform again to make the probe return to the (0,0) position, and after the system stabilizes, drop the needle at this position to deliver "AAAAAA" ink to the substrate surface, completing the writing of an "A" nanodot.

[0070] Then, use a syringe to transfer ultrapure water to the edge of the mica sheet. Next, move the flexible platform to allow the probe to pick up the ultrapure water, and then move the flexible platform again to return the probe to its initial position, completing one needle washing process.

[0071] Then, the "TTTTTT" ink is transferred to the edge of the mica sheet using a syringe. The flexible platform is then moved to allow the probe to pick up the "TTTTTT" ink. The platform is moved again to return the probe to the spotting position. Once the system stabilizes, the probe is dropped into this position, delivering the "TTTTTT" ink onto the substrate surface, completing the writing of a "T" nanodot. Figure 5 As shown, after writing a nanodot is completed, the needle is washed again.

[0072] 3. Read: Using a syringe, transfer "AAAAAA" ink to the edge of the mica sheet. Then, move the flexible platform to allow the probe to pick up the "AAAAAA" ink. Move the platform again to return the probe to the upper nanodot position. After the system stabilizes, move the probe downwards to test the force curve of the upper nanodot within the 5-200 nm range. Then, move the platform again to return the probe to the lower nanodot position. After the system stabilizes, move the probe downwards to test the force curve of the lower nanodot within the 5-200 nm range. Figure 5 As shown, the force curves of the lower nanodots show a significant shift compared to the upper nanodots. This phenomenon is caused by the base pairing forces, which proves that the upper nanodots are "A" and the lower nanodots are "T".

[0073] 4. Decoding: By using the "simple mapping" method to restore the encoding again, the quaternary "AT" can be restored to the binary "0010", thus completing the information reading.

[0074] In summary, this invention provides a method and application for array-based DNA information storage, which includes first converting the digital information to be stored into binary "0, 1" codes, and then encoding the binary "0, 1" codes into quaternary "adenine (A), guanine (G), thymine (T), cytosine (C)" codes. A strategy combining atomic force microscopy (AFM) and a flexible nanoplatform is used to write DNA nanodots. Figure 2 As shown, different types of DNA ink can be transferred to the substrate edge using a syringe and capillary tube. A movable, flexible nanoplatform enables the picking up of DNA ink and the writing of DNA nanodots. During information reading, base identification can be performed using specific methods (base pairing force curves, hybridization color development, etc.). Finally, the identified "A, G, T, C" codes are converted into binary "0, 1" codes, and then into corresponding digital information. The DNA information storage method of this invention helps improve the accuracy of DNA information reading and the read / write speed of DNA storage, and it also offers good security and promising application prospects.

[0075] The embodiments of the present invention have been described in detail above. However, the present invention is not limited to the above embodiments. Within the scope of knowledge possessed by those skilled in the art, various changes can be made without departing from the spirit of the present invention. Furthermore, the embodiments of the present invention and the features thereof can be combined with each other unless otherwise specified.

Claims

1. A method for storing array-based DNA information, characterized in that, Includes the following steps: S1. The information to be stored is converted into a binary sequence using an encoding algorithm, and the binary sequence is converted into a base sequence according to a preset mapping relationship; S2. Prepare DNA ink containing the base sequence, then transfer it to the edge of the substrate material, move the flexible platform to make the probe contact the DNA ink, and then drop the probe at the first preset position on the substrate material and lift the probe to obtain DNA nanodots containing the information to be stored, thereby realizing DNA information storage.

2. The array-dot DNA information storage method according to claim 1, characterized in that, The information to be stored includes at least one of the following: images, text, programs, audio, and video.

3. The array-based DNA information storage method according to claim 1, characterized in that, The concentration of the DNA ink is 10-100 µM; And / or, the solvent of the DNA ink is selected from any one of water, phosphate buffer, or physiological saline; And / or, the volume of the DNA ink transferred is 10-1000 µL.

4. The array-dot DNA information storage method according to claim 1, characterized in that, The substrate material is selected from any one of mica sheets, polished silicon wafers, glass sheets, or graphite; And / or, the distance between the edge of the substrate material and the substrate material is 0-1000 µm.

5. The array-dot DNA information storage method according to any one of claims 1-4, characterized in that, Before the probe comes into contact with the DNA ink, the substrate material is scanned using an atomic force microscope. Preferably, the scanning range is 1-10000 µm. 2 ; Preferably, the roughness of the substrate material is ≤5 nm.

6. The array-dot DNA information storage method according to claim 5, characterized in that, The flexible platform has a movement range of 10-1000 µm; And / or, the probe contacts the DNA ink for 1-50 s; And / or, the time for the needle to fall at the first preset position is 10-100 s.

7. The array-based DNA information storage method according to claim 5, characterized in that, After obtaining the DNA nanodots containing the information to be stored, the process also includes washing the needle. And / or, by replacing the DNA ink and the first preset position, repeat step S2 to prepare the second DNA nanodot.

8. A method for reading information stored in array-dot DNA, characterized in that, The array-dot DNA information obtained by the array-dot DNA information storage method according to any one of claims 1-7 is subjected to base identification using a base pairing force curve or a hybridization colorimetric method, and then read according to the preset mapping relationship.

9. A storage system, characterized in that, It includes a storage unit and a reading unit, wherein the storage unit operates the array-dot DNA information storage method as described in any one of claims 1-7.

10. The application of the array-dot DNA information storage method as described in any one of claims 1-7 or the array-dot DNA storage information reading method as described in claim 8 in DNA data storage.

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