A logic element based on DNA nanostructure and application thereof

Abstract

The application belongs to the field of biological computer technology and DNA nanotechnology, and particularly relates to a logic element based on a DNA nanostructure and application of the logic element in manufacturing a true random number generator. The logic element based on the DNA nanostructure takes a two-dimensional cross DNA nanostructure as a main body of the element, utilizes basic characteristics of the DNA nanostructure, such as uniform size, accurate site programming and rich extensible edge chains, constructs logic elements carrying different information through site programming, takes the extensible edge chains as sticky ends to realize a stable and reliable coaxial physical connection relationship between the logic elements, and only when there is a complementary relationship between the sticky ends of the logic elements, can a dimer or a multimer be formed through self-assembly. Therefore, when the logic element is applied to manufacturing the random number generator, the multimer connected by the cross paper folds still has good rigidity, and the correctness of the random generation result is ensured.

Description

TECHNICAL FIELD

[0001] The application belongs to the field of biological computer technology and DNA nanotechnology, and particularly relates to a logic element based on a DNA nanostructure and application of the logic element in manufacturing a true random number generator. BACKGROUND

[0002] Today, with the rapid development of information technology, the demand for random numbers is increasing. Traditional computer random number generators are mostly pseudo-random number generators, and the results are determined by a certain algorithm and initial seed, which has a certain predictability. Since all software algorithms for generating random values work based on mathematical formulas, their output will appear in a pseudo-random form. Even the strongest formula will repeat the output after a period of time. In some fields with extremely high requirements for randomness, such as cryptography, quantum physics research, secure communication and Monte Carlo simulation, such pseudo-randomness may cause security risks or affect the accuracy of simulation results. Therefore, it is an urgent need to find a true random number generation method.

[0003] The process of generating a true random number is truly random and does not allow the generated sequence to be predicted in any way. These generators are called true random number generators (TRNG). In order to generate a true random value, the demand for a natural noise source means that the noise source can be reliably used for a random number generator only when it comes from a physical environment. For example, the patent with publication number CN106687916B discloses a random number generator for obtaining a true random number sequence by a quantum mechanism of generating photons by a light source, which has the uncertainty of measurement events as an inherent property of the quantum system itself. However, the generation of random numbers is first obtained by an electronic sampling device to obtain a photon source, and then the binary sequence is processed by a von Neumann algorithm, and the randomness of the algorithm is also required to judge the randomness of the random number generation result, which cannot be directly observed.

[0004] DNA origami is a technique that uses the special structure of DNA molecules and the rules of base pairing to fold specific regions of long DNA chains and fix them with short chains to construct the desired structure. Referring to the reference "Folding DNA to create nanoscale shapes and patterns. Nature, 2006, 440: 297-302", in 2006, a research team at the California Institute of Technology successfully used DNA origami to assemble the genomic DNA of bacteriophage M13 as a long chain with more than 200 short single-stranded DNA through the principle of base complementary pairing to form a variety of two-dimensional patterns such as rectangles, triangles, pentagons, and smiley faces. DNA origami technology has unique properties and provides a new way of thinking for random number generation. The self-assembly process of DNA molecules is affected by various factors, including temperature, ion concentration, solution pH, and small changes in these factors can lead to different assembly results, which means that DNA origami technology can generate structures with high uncertainty, and thus it is possible to obtain true random numbers. Moreover, DNA as a biological molecule has high stability and operability, providing a reliable material basis for random number generation and storage. SUMMARY

[0005] To solve the above technical problems, the present application mainly provides a logic element based on DNA nanostructure, which uses a two-dimensional cross DNA nanostructure as the main body of the element. The basic characteristics of the DNA nanostructure are uniform size, precise site programming, and rich extensible edge chains. The logic element carrying different information is constructed by site programming. The extensible edge chain serves as a sticky end to achieve a stable and reliable physical connection relationship between the logic elements. The cross origami of the connection relationship is coaxial, and only when there is a complementary relationship between the sticky ends of the logic elements, a dimer or a multimer can be formed through self-assembly by one-pot annealing. Based on the above logic element, the present application also provides its application in generating random numbers.

[0006] In a first aspect, a DNA nanostructure-based logic element is provided, which is a two-dimensional cross-shaped DNA nanostructure. At present, most two-dimensional DNA nanostructures are prepared by DNA origami. The two-dimensional cross-shaped DNA nanostructure is also assembled from a DNA template strand and DNA staple strands by DNA origami. The DNA template strand serves as a main chain, and the excess DNA staple strands serve as auxiliary chains. The main chain and the auxiliary chains are hybridized and complementary at specific positions, thereby assembling the two-dimensional cross-shaped DNA nanostructure. In the selection of the DNA template strand, the M13mp18 bacteriophage genomic DNA sequence provided in GenBank: X02513.1 is preferred. The DNA staple strands serve as auxiliary chains, wherein part of the DNA staple strands are programmable auxiliary chains, i.e., functional DNA staple strands, and the remaining DNA staple strands are non-functional DNA staple strands. Part of the functional DNA staple strands are used to generate sticky end chains after subsequent assembly. This part of the functional DNA staple strands is denoted as sticky DNA chains. After assembly, a plurality of free sticky end chains extend from one side or both sides of the edge of the main body of the two-dimensional cross-shaped DNA nanostructure. These sticky end chains form a sticky end chain group. The base sequences of the sticky end chains in the sticky end chain group are all different from each other, so as to ensure that the two-dimensional cross-shaped DNA nanostructure maintains a high specific recognition ability and a high self-assembly yield. Preferably, there are six sticky end chains in the sticky end chain group, which are uniformly distributed on one side of the edge of the main body of the two-dimensional cross-shaped DNA nanostructure. Another part of the functional DNA staple strands is denoted as a DNA capture chain. The DNA capture chain comprises two blocks. One part of the block serves as a staple chain for the assembly of the main body of the two-dimensional cross-shaped DNA nanostructure. The other part is used to extend at least one capture sequence for capturing a marker structure on the surface of the main body of the two-dimensional cross-shaped DNA nanostructure after assembly. The capture position is the site of the logic element for carrying information. Preferably, the capture sequence is a nucleotide sequence added at the 5' end of the DNA staple chain. Further preferably, the capture sequence is a 10-nucleotide length sequence, which is used to accurately control the number and relative position of the marker structure on the two-dimensional cross-shaped DNA nanostructure. The marker structure is selected from any one of nanogold-mercapto-oligonucleotide, streptavidin SA, and a fluorescent group. If the marker structure is nanogold-mercapto-oligonucleotide, the capture structure is a sequence complementary to the oligonucleotide in the nanogold-mercapto-oligonucleotide. Preferably, in order to take advantage of the strong affinity and fast binding speed between SA and biotin, the marker structure is preferably SA, the capture sequence is a biotin-modified capture sequence, and the DNA capture chain is a biotin-modified DNA capture chain.

[0007] The two-dimensional cross DNA nanostructure has the programmable characteristics of all sites, can be used as a carrier of information, and the cross structure is beneficial to distinguish different sites, for example, as a preferred embodiment of the logic element described in the present application, as shown in Figure 2a The specific sites for capturing the marking structure on the two-dimensional cross DNA nanostructure include information sites and check sites, the information sites representing different numbers are arranged above and below the horizontal line of the cross structure, which is beneficial to the observer to distinguish the information sites on the nanoscale level and thus is beneficial to quickly read the information; in addition, in order to meet the requirement that a single two-dimensional cross DNA nanostructure can represent two-digit numbers, the information sites representing different digit numbers are arranged on the left and right sides of the cross structure as high bits and low bits, respectively, and the left and right sides are distinguished by the check sites, which are arranged on one side of the main body of the two-dimensional cross DNA nanostructure to determine the direction of information reading, and the high bits are read first and then the low bits when reading the number, thereby ensuring the accuracy of information reading; when reading, if all the information sites representing the same digit number are all without marking structures or all have marking structures, it is error data, and only one information site representing the same digit number has a marking structure is correct data, and correspondingly, 5 capture sequences are arranged on the DNA nanostructure, and one capture sequence captures one marking structure.

[0008] As a preferred embodiment, the size of the two-dimensional cross DNA nanostructure is set to 100 nm in length and 100 nm in width; as shown in Figure 1 The preparation process of the logic element based on the DNA nanostructure of the first aspect includes the following steps: step S1, mixing the DNA template chain, the functional DNA staple chain and the non-functional DNA staple chain in a buffer solution for PCR annealing to obtain a two-dimensional cross DNA nanostructure; step S2, ultrafiltration purification of the annealing product obtained in step S1 to replace the buffer solution to obtain the logic element based on the DNA nanostructure.

[0009] Preferably, in step S1, the PCR annealing conditions are as follows: the starting temperature is 95℃, maintained for 3 minutes, and the end temperature is 25℃, with 1℃ as a gradient, and each gradient stays for 100s.

[0010] Preferably, in step S1, the molar ratio of the DNA template chain, the non-functional DNA staple chain and the functional DNA staple chain is 1:10:10.

[0011] Preferably, in step S2, the ultrafiltration purification is performed three times, and the ultrafiltration conditions are 3000xg for 8 minutes each time.

[0012] Preferably, the buffer in step S1 is 1×TAE / Mg 2+ ;

[0013] Preferably, the step of ultrafiltration in step S2 is to mix the obtained annealing product with 1×TAE / Mg 2+ buffer and add a 100 kDa ultrafiltration tube, and centrifuge.

[0014] In view of the basic characteristics of the logic element based on DNA nanostructure provided in the first aspect of the present application, which are site programmable, stable connection relationship between logic elements can be formed through sticky end complementarity, and the connection relationship can be saved, the present application further applies it to generate true random numbers, i.e. the second aspect, the present application also provides an application of the logic element based on DNA nanostructure in making a true random number generator, and the specific application includes the following steps:

[0015] Step S1, obtain preset conditions according to the type of random number to be generated, and then make or select different logic elements based on DNA nanostructure according to the preset conditions; it should be noted that the differences here include different information represented by sites and different sticky end group settings;

[0016] The preset conditions obtained according to the type of random number to be generated refer to: according to the number of digits of the random number to be generated, determine the combination times of different numbers, and then according to the combination times, determine the number of logic elements with connection relationship, i.e. the value of N in N-mer, whether it is dimer or multimer, has good rigidity, which can ensure that the randomly generated results can be stored in the correct order and will not be wrong.

[0017] The different sticky end group settings refer to single left setting, single right setting or both sides setting; the two-dimensional cross DNA nanostructure is matched and connected through the base complementary relationship of the sticky end group on both sides of the cross paper folding;

[0018] The connection relationship between the logic elements representing numbers is random through the setting of the sticky end group, and in addition, all the logic elements are self-assembled under the same physical environmental conditions, so that the combination between numbers based on the logic elements is random; for example, in the random number generation based on dimer, when setting the sticky end group, in order to ensure that the sticky end group on the two-dimensional cross DNA nanostructure has an equal competitive relationship, such as Figure 3As shown, the sticky end group arranged at the left side of the logic element is L group, and the six sticky end chains of the L group are L1, L2, L3, L4, L5 and L6 respectively. The sticky end group arranged at the right side of the logic element is R group, and the six sticky end chains of the R group are R1, R2, R3, R4, R5 and R6 respectively. The sticky end groups at the left side of different logic elements are all the six sticky end chains of the L group, and the sticky end groups at the right side of different logic elements are all the six sticky end chains of the R group. The six sticky end chains of the L group and the six sticky end chains of the R group correspond to each other, and have base complementary relationship, which represents the relationship of random number generation.

[0019] In step S2, different DNA nanostructure-based logic elements are mixed in equal proportions, and an assembly product is obtained by annealing self-assembly in PCR. SA is added to the assembly product for connection, and a multimer with a marker structure formed thereby is used as a random number generator. The generation result can be directly observed by atomic force microscopy (AFM). Preferably, the annealing conditions are as follows: starting temperature 45°C, and slowly annealing in water bath to end temperature 25°C. Preferably, the obtained annealing product is diluted to 1-2 nM. Preferably, the obtained diluent is added to SA, and the molar concentration of the site to SA is 1:50.

[0020] Further preferably, the application of the DNA nanostructure-based logic element in the preparation of a true random number generator further comprises step S3 of detecting and judging whether the generation result of the random number generator is completely random. The detection means mainly include frequency test, run test and sequence test. Specifically, the detection and judgment process is to perform sample morphology characterization by atomic force microscopy (AFM) to obtain an AFM graph. The generation result of the random number is mainly counted by objective observation. All samples in the generated AFM graph are counted one by one. If there are some error structures in the samples, they will be checked and excluded from the generation result. Finally, the results are summarized and the proportion of each result is calculated. The frequency test mainly checks the proportion of 0 and 1 in the whole sample. If the proportion is the same, the test is passed. The run test mainly checks the total number of runs. A run refers to a sequence of the same number without interruption, for example, “1111” or “0000” in a four-bit random number generator. The proportion of continuous 0 or 1 in the total number of the two samples is counted. The sequence test (two-bit-test): the main purpose of this test is to find out whether the number of all results is approximately the same, i.e., the proportion of all possibilities in the total number of samples.

[0021] For example, in the preparation of a two-bit random number generator, as shown in FIG. 2, the logic element is a two-bit random number generator, and the logic element is a two-bit random number generator. Figure 4aAs shown in the figure, each logic element only represents a bit of number, and the encoding information is 0 or 1, and a dimer is assembled by connecting chains on the left and right sides of the logic element, the dimer represents a random combination of two bits of information, i.e. two bits of random number, and through the AFM graph of the randomly obtained two bits of random number, the samples in all obtained AFM graphs are counted, and then statistical tests are carried out according to the requirements of frequency test, run test and sequence test.

[0022] For example, in the production of a four-bit random number generator, as shown in the figure, Figure 5a As shown in the figure, the cross paper has two bits of information encoding 00, 01, 10 and 11, and a dimer is assembled by connecting chains on the left and right sides, and at this time the dimer represents four bits of information, i.e. four bits of random number, and through the AFM graph of the randomly obtained four bits of random number, the samples in all obtained AFM graphs are counted, and then statistical tests are carried out according to the requirements of frequency test, run test and sequence test.

[0023] For example, in the production of an eight-bit random number generator, as shown in the figure, the cross paper has two bits of information encoding 00, 01, 10 and 11, and a tetramer is assembled by connecting chains on the left and right sides, and at this time the tetramer represents eight bits of information, i.e. eight bits of random number, and in the generation of the eight bits of random number, the connecting chains have three groups, each of which corresponds to one, and is used to ensure the accuracy of the connection and to generate only the tetramer.

[0024] As a preferred embodiment, in order to improve the connection yield, the connecting chains of the cross paper are 0.5 times more than the calculated amount, and the connection yield is as high as 90%, and the excess connecting chains in the assembled cross paper are removed by ultrafiltration, and more connecting chains are used to solve the problem of the connection yield;

[0025] According to the same technical concept as the second aspect, the third aspect of the present application also provides a kind of true random number generator, and the true random number generator is used to generate random number, and the true random number generator comprises:

[0026] The encoding module is used to obtain preset conditions according to the type of random number to be generated, and then different DNA nanostructure-based logic elements are made or selected according to the preset conditions;

[0027] The logic element database is used to store the different DNA nanostructure-based logic elements described above;

[0028] The reaction platform is connected with the logic element database and provides suitable reaction conditions, and is used to mix the different DNA nanostructure-based logic elements under the same physical environmental conditions, so that self-assembly reaction occurs to obtain a reaction product;

[0029] A result obtaining module is configured to observe the reaction product and the reaction result, and to determine whether the generated result of the random number generator is completely random.

[0030] In a fourth aspect, the application further provides an application of the true random number generator in information encryption.

[0031] Beneficial effects:

[0032] The molecular motion behavior of DNA molecules provides a pure physical noise source, which can be used to generate high-quality true random values.

[0033] The first aspect of the application provides a kind of logic element based on DNA nanostructure, which uses DNA nanostructure as DNA computing element, and the uniform size of the designed DNA nanostructure, the programmable site of recombination provides accurate site design, and the rich extensible side chain can provide stable and reliable physical connection relationship;The left and right single measurement of two-dimensional cross DNA nanostructure or the sticky end chain extended from both sides can make random connection between cross paper folds;Based on the above-mentioned logic element, the cross paper plate with connection relationship is coaxial, and when applied to random number generation, the multimer connected by multiple cross paper plates can still have good rigidity, so as to ensure that the generation result can be stored in correct order without error, so as to observe the subsequent calculation result, and the above-mentioned logic element has encryption ability and storage capacity.

[0034] The second aspect and other aspects of the application provide the application of the above-mentioned logic element based on DNA nanostructure in random number generation, on the basis of experimental verification, the research personnel of the subject group continuously improve and optimize the random number generation technology based on DNA paper folding, on the one hand, the design and assembly method of DNA paper folding is improved, the complexity and diversity of its structure are improved to increase the entropy value of random number, on the other hand,

[0035] In combination with other technologies such as nanotechnology, optical technology, etc., the efficiency and accuracy of random number generation are improved. For example, the structure of DNA origami is controlled by light stimulation to achieve more accurate random number generation. With the continuous maturity of technology, DNA origami-based random number generation technology has begun to be applied in various fields. In the field of cryptography, DNA origami random numbers can be used in encryption algorithms to improve the security of information. Compared with other algorithms, it has the following advantages: 1. Large key space: DNA origami encryption technology can use very long DNA chains as keys, for example, a skeleton chain of about 7000 bases can achieve a theoretical key length of about 700 bits, which is much higher than the key strength of traditional encryption algorithms such as AES. Such a large key space makes brute force cracking almost impossible, greatly improving the security of encryption. 2. Biological molecule-based encryption is performed through a biologically molecule reaction controlled by thermodynamics, which has high specificity. DNA, as a biological molecule, has a unique structure and reaction, which is completely different from the encryption system based on silicon-based computers, making it difficult for hackers to use conventional computer technology and algorithms to crack DNA origami encrypted information, avoiding attacks from computers. 3. DNA origami encryption can hide information in the structure and sequence of DNA, which is very difficult to detect. Compared with traditional encryption methods, information is less likely to be discovered and stolen during transmission and storage, realizing the integration of cryptography and steganography. 4. DNA itself has a huge information storage capacity, which is 5 million times that of current storage methods. 5. DNA molecules have high stability and resistance to physical and chemical environmental disturbances. In contrast, some traditional encryption technologies may be affected by electromagnetic interference, temperature changes, and other factors, resulting in loss or damage of information. DNA origami encryption technology can better protect the security of information in complex environments. In quantum physics research, it can be used as a random number source for quantum experiment simulation and verification; in the field of biomedicine, it can also be used for randomized experimental design and data analysis, etc. Moreover, researchers are also exploring new application fields, such as applications in artificial intelligence, big data, etc., providing more reliable random number support for the development of these fields.

[0036] The two-dimensional cross-shaped DNA nanostructure mainly used in the application has good biocompatibility, and other required chemical and biological materials also have no human body toxicity. BRIEF DESCRIPTION OF DRAWINGS

[0037] Figure 1 A synthesis diagram of the two-dimensional cross-shaped DNA nano encryption element described in the application;

[0038] Figure 2a A diagram of information site setting and its representative information in the specific embodiment of the application and a yield statistical diagram of each information.

[0039] Figure 2b Schematic diagram of logical elements corresponding to 0, 1 encoding information in Example 1 and characterization photos;

[0040] Figure 2c Logical elements and characterization photos corresponding to 00, 10, 01, 11 encoding information in Example 2;

[0041] Figure 2d Yield of logical elements corresponding to 0, 1, 00, 10, 01, 11 encoding information in Example 1 and Example 2;

[0042] Figure 3 Schematic diagram of distribution of sticky DNA strands on logical elements in Example 1;

[0043] Figure 4a Schematic diagram of two-bit random number generation process in Example 1;

[0044] Figure 4b Dimer structure morphology characterization diagram obtained by two-bit random number generation in Example 1;

[0045] Figure 4c Frequency test statistical diagram of two-bit random number generation results in Example 1;

[0046] Figure 4d Run test of two-bit random number generation results in Example 1;

[0047] Figure 4e Sequence test statistical diagram of two-bit random number generation results in Example 1;

[0048] Figure 5a Schematic diagram of four-bit random number generation process in Example 2;

[0049] Figure 5b Dimer structure morphology characterization diagram obtained by four-bit random number generation in Example 2;

[0050] Figure 5c Frequency test statistical diagram of four-bit random number generation results in Example 2;

[0051] Figure 5d Run test statistical diagram of four-bit random number generation results in Example 2;

[0052] Figure 5e Sequence test statistical diagram of four-bit random number generation results in Example 2;

[0053] Figure 6a Schematic diagram of eight-bit random number generation constructed in Example 3;

[0054] Figure 6b Figure 1 shows the tetramer structure topography characterization map obtained for the eight-bit random number generation in Example 3;

[0055] Figure 7 Figure 2 shows the encryption and decryption schematic diagram using the codebook constructed in Example 3. DETAILED DESCRIPTION

[0056] In order to further illustrate the technical means adopted by the present application and its effects, the present application will be further described below in conjunction with the embodiments and drawings. It can be understood that the specific embodiments described herein are only used to explain the present application, and not to limit the present application.

[0057] The raw materials and reagents used in the following preparation process and examples are described as follows:

[0058] Tris, disodium EDTA, magnesium acetate, glacial acetic acid, boric acid were purchased from National Pharmaceutical Group Chemical Reagent Co., Ltd.; 100 kDa ultrafiltration tube was purchased from pall China company; experimental water was ultrapure water.

[0059] M13mp18 bacteriophage genomic DNA was purchased from Bio- Basic Inc., with the item number and specification of B3003-50pmol; non-functional DNA staple chain, functional DNA staple chain, biotin-ssDNA chain and streptavidin were purchased from Shanghai Sangon Biological Engineering Co., Ltd.

[0060] Unless otherwise specified in the examples, the techniques or conditions were carried out according to the techniques or conditions described in the literature in the art, or according to the product instructions. Unless otherwise specified, the reagents or instruments used were conventional products that can be commercially available through regular channels.

[0061] Specifically, the preparation process of the DNA nano-encryption element and its application in the preparation of a random number generator are described in detail with the preparation of a two-bit, four-bit and eight-bit random number generator as an example.

[0062] Example 1: Preparation of a two-bit random number generator

[0063] As a preferred embodiment of the two-bit random number generation method of the present application, the specific steps of Example 1 include:

[0064] According to the preset conditions required for two-bit random number generation, the sticky ends of the two-dimensional cross DNA nanostructure are encoded with DNA sequences and the two-dimensional cross DNA nanostructure is labeled with a label structure to construct a variety of different logic elements. The preset conditions of this embodiment include the number represented by each logic element and the connection relationship between the crosses.

[0065] In the embodiment, five DNA capture chains are anchored on the surface of the two-dimensional cross-shaped DNA nanostructure, one chain captures one SA, and the two-dimensional cross-shaped DNA nanostructure is formed by self-assembly of M13mp18 template chains and staple chains. The DNA sequence of the M13mp18 template chain is provided in GenBank: X02513.1, and the non-functional DNA staple chain used in the two-dimensional cross-shaped DNA nanostructure can be found in the document “Crystalline two-dimensional DNA-origami arrays. Angew Chem Int Ed Engl. 2011 Jan 3; 50(1): 264-7.”. The DNA capture chain is a non-functional DNA staple chain in the above document, and a capture sequence with biotin modification is added at the end of the non-functional DNA staple chain. Different information sites are encoded by controlling the modification of biotin. The sequence number of the non-functional DNA staple chain in the above document and the corresponding information site number of the present application are as follows: site 1 corresponds to the position of CO-M-95 in the document, site 2 corresponds to the position of CO-M-90 in the document, site 3 corresponds to the position of CO-M-166 in the document, site 4 corresponds to the position of CO-M-171 in the document, and site 5 corresponds to the position of CO-M-154 in the document. The nucleotide sequences of the five capture sequences are shown as SEQ ID NOs: 1-5.

[0066] The sticky DNA chain is a non-functional DNA staple chain in the above document, and a corresponding sticky end is added at the end of the non-functional DNA staple chain. The sticky end is the connecting chain in Table 1, which is connected to the sequences of CO-A-L1-CO-A-L6 and CO-A-R1-CO-A-R6 in the above document as sticky DNA chains, as shown in Figure 3 After a large number of experiments, it is verified that the connection yield of the six connecting chains is the best. The sticky end group of each group of sticky end groups extends on the left and right sides of the cross-shaped origami DNA nanostructure. It should be noted that, in order to simplify the schematic diagram, Figure 3 in the same group of sticky end groups, each sticky end group is represented by a thick line, and the thick lines with the same linear mark on the same side belong to a group of sticky end groups. In order to form this sticky end structure, the two-bit random number generator is specifically designed as shown in Table 1:

[0067] Six connecting strands Left connecting strand Right connecting strand First connecting strand L1 : SEQ ID NO: 6 R1 : SEQ ID NO: 12 Second connecting strand L2: SEQ ID NO: 7 R2: SEQ ID NO: 13 Third connecting strand L3: SEQ ID NO: 8 R3: SEQ ID NO: 14 Fourth connecting strand L4: SEQ ID NO: 9 R4: SEQ ID NO: 15 Fifth connecting strand L5: SEQ ID NO: 10 R5: SEQ ID NO: 16 Sixth connecting strand L6: SEQ ID NO: 11 R6: SEQ ID NO: 17

[0068] As shown in Figure 2aAs shown in the figure, information site 1 and information site 2 represent information 0, and information site 1 is low, and information site 2 is high; information site 3 and information site 4 represent information 1, and site site 3 is low, and site site 4 is high; site 5 represents information check bit Marker, which is used to mark the direction of the cross paper folding, and judge whether the paper folding belongs to the normal position;

[0069] As shown in the figure, there is only one bit of information on the cross paper folding, which is 0 or 1, and the left and right side connecting chains are assembled into a dimer, which represents two bits of information, that is, a two-bit random number; Figure 4a

[0070] According to the above preset conditions, for two-bit random number generation, and considering the site information of the logic element and the sticky end setting, four kinds of logic elements need to be prepared, and each logic element is operated according to the following steps:

[0071] (1) Mix M13mp18 template chain, non-functional DNA staple chain and DNA functional chain. The final concentration of the template chain and all DNA staple chains is 5uM and 50nM respectively.

[0072] (2) Slowly anneal the mixture using a gradient PCR instrument. The annealing conditions are: the starting temperature is 95℃, and the holding time is 3 minutes; the end temperature is 25℃, and each gradient stays for 100 seconds with every 1℃ as a gradient, so as to obtain a two-dimensional cross DNA nanostructure;

[0073] (3) After the annealing program is completed, the two-dimensional cross DNA nanostructure sample is taken out, and 100kDa centrifugal tube is used for centrifugal separation to remove excess DNA short chain. The centrifugal conditions are: 300μL 1×TAE-Mg2+buffer solution is added to 100μL sample, and centrifuged at 2800rcf / min for 8 minutes, and the centrifugal operation is repeated three times.

[0074] Characterization of logic element: in order to clearly characterize the logic element used in this embodiment 1, the two-dimensional cross DNA nanostructure obtained by the above preparation is added with a labeled structure SA, and the specific operation is: the two-dimensional cross DNA nanostructure obtained by preparation is mixed with SA at a molar ratio of 1:50 and then annealed and incubated for 24 hours, and the annealing conditions are: the starting temperature is 37℃, and the end temperature is 25℃, every 1℃ as a gradient, and each gradient stays for 10 minutes, and the annealing time is kept for 2 hours; the obtained annealing product is ultrafiltrated and the buffer solution 1×TAE / Mg 2+ and the ultrafiltration step is to replace the obtained annealing product with 1×TAE / Mg 2+ ​The buffer was mixed and added to a 100 kDa ultrafiltration tube to ultrafiltrate and remove excess SA. The purified cross-plate DNA nanometer encryption element was obtained by centrifugation at 3000 x g for 8 minutes. The final collected sample was observed for sheet structure morphology by atomic force microscopy (AFM), as shown in Figure 2b The two logic elements corresponding to the encoding information 0 and 1 are shown, and the constructed DNA nanostructure is a cross-plate sheet structure. AFM characterization results show that the rectangular two-dimensional DNA nanostructure is about 100 nm long and about 100 nm wide, and presents a regular cross structure.

[0075] The four logic elements prepared above were mixed in equal molar ratio, and the concentration of each logic element was 3 nM. The mixed solution system was 80 uL. The annealing was performed in a PCR for 14 hours. The annealing was performed in a water bath, and the temperature was slowly reduced from 45 °C to 25 °C. After the annealing program was completed, the obtained annealing product was diluted to 1-2 nM. The obtained diluent was added to SA, i.e., the structure SA was labeled on the above-mentioned logic element formed duplex structure. The specific operation was the same as that of the specific operation of labeling the structure SA in the above-mentioned logic element characterization;

[0076] The obtained duplex structure was characterized by AFM for morphology, as shown in Figure 4b The obtained duplex structure is shown in part of the observation view. The statistical results of the generated results were randomly detected to determine whether the random number generation results were completely random. The frequency test results are shown in Figure 4c The run test results are shown in Figure 4d The sequence test results are shown in Figure 4e

[0077] Example 2: Preparation of a four-bit random number generator

[0078] The difference between Example 2 and Example 1 is that in the four-bit random number generation, as shown in Figure 5a Each cross origami has two-digit encoding information, which is 00, 01, 10, and 11, respectively. The two-digit information is assembled into a duplex by the left and right connecting chains. At this time, the duplex represents four digits, i.e., a four-bit random number.

[0079] For example, the encoding information 01 corresponds to the information sites 1 and 4 and the check site 5 with the label structure captured. The encoding information 10 corresponds to the information sites 2 and 3 and the check site 5 with the label structure captured. When 01 and 10 appear at the same time, it is difficult to distinguish without the label of the check site 5. With the check site 5, the origami direction can be adjusted according to the direction of the check site 5 to determine the information represented by the origami.

[0080] As shown in Figure 2c ​As shown in the production of logic elements in Example 1, the logic elements corresponding to the four encoding information 00, 10, 01 and 11 are respectively produced; as shown in Figure 2d As shown in the production of logic elements in Example 1 and Example 2, the logic elements corresponding to the six encoding information 0, 1, 00, 10, 01 and 11 are respectively produced.

[0081] In the four-bit random number generation, the cross DNA nanometer encryption elements with connecting chains and encoding information 00, 01, 10 and 11 are mixed in equal molar ratio and uniformly mixed. Put into a water bath and anneal, slowly from 45°C to 25°C, after the annealing program is finished, the obtained annealing product is diluted to 1-2nM, and AFM is used for topographic characterization, as shown in Figure 5b As shown in the characterization diagram of the correct results of the cross plate polymer, by statistical analysis of a plurality of AFM characterization diagrams, frequency test, run test, sequence test are carried out to determine whether the random number generation result is completely random. The frequency test result is as shown in Figure 5c As shown, the run test result is as shown in Figure 5d As shown, the sequence test result is as shown in Figure 5e As shown.

[0082] Example 3: Production of eight-bit random number generator

[0083] The difference between Example 3 and Example 2 is that there are three groups of connecting chains, and the connecting chain sequences are as shown in

[0084] SEQ ID NO: 6-41, SEQ ID NO: 6-17 is a group, SEQ ID NO: 18-29 is a second group,

[0085] SEQ ID NO: 30-41 is a third group, and each group of connecting chains is respectively connected to the sequences of C0-A-L1-C0-A-L6 and C0-A-R1-C0-A-R6 in the above document as the sticky DNA chain;

[0086] In the eight-bit random number generation, the same information encoding method as in the four-bit random number generation method in Example 2 is used, as shown in Figure 6a As shown, there are two information encodings 00, 01, 10 and 11 on the cross paper, and the difference is that this embodiment 3 is assembled into a tetramer through the left and right connecting chains, at this time the tetramer represents eight-bit information, that is, eight-bit random number, in the eight-bit random number generation, it has three groups of connecting chains, each corresponding to one, to ensure the accuracy of the connection and only generate tetramer.

[0087] In the generation of eight random numbers, cross-shaped DNA nanofibers with connecting strands and encoded information of 00, 01, 10, and 11 were mixed in an equimolar ratio and annealed in a water bath, slowly decreasing from 45°C to 25°C. After the annealing process, the resulting annealed product was diluted to 1–2 nM and its morphology was characterized using AFM. Figure 6b As shown, an eight-bit random number generator can be used as a codebook for encryption and decryption.

[0088] Example 4: An 8-bit random number generator for encryption and decryption

[0089] By listing the tetramer reading information from the AFM diagram in the 8-bit random number generator into the codebook, such as... Figure 7 As shown, the binary information represented by the tetramer generated by the eight-bit random number generator can be used as a key for encryption and decryption. During the encryption process, the key can be randomly selected for encryption.

[0090] The applicant declares that the detailed method of the present invention is illustrated by the above embodiments, but the present invention is not limited to the above detailed method, that is, it does not mean that the present invention must rely on the above detailed method to be implemented. Those skilled in the art should understand that any improvements to the present invention, equivalent substitutions of the raw materials of the product of the present invention, addition of auxiliary components, selection of specific methods, etc., all fall within the protection scope and disclosure scope of the present invention.

Claims

1. A DNA nanostructure-based logic element, characterized in that, The logic element is a two-dimensional cross DNA nanostructure, which is assembled by DNA template chains and DNA staple chains through DNA origami, the DNA template chains serve as main chains, and the excess DNA staple chains serve as auxiliary chains, the main chains and the auxiliary chains are hybridized and complementary at specific positions, and then the two-dimensional cross DNA nanostructure is assembled; part of the DNA staple chains are programmable auxiliary chains, i.e., functional DNA staple chains, and the remaining DNA staple chains are non-functional DNA staple chains; part of the functional DNA staple chains are used to generate sticky end chains after subsequent assembly, and this part of the functional DNA staple chains is recorded as sticky DNA chains, after assembly, a plurality of free sticky end chains extend from one side or both sides of the main body of the two-dimensional cross DNA nanostructure, and the sticky end chains form a sticky end group, the base sequences of the sticky end chains in the sticky end group are all different from each other; the other part of the functional DNA staple chains are DNA capture chains, the DNA capture chains include two blocks, one part of the blocks serves as a staple chain for the assembly of the main body of the two-dimensional cross DNA nanostructure, and the other part is used to extend at least one capture sequence for capturing a label structure on the surface of the main body of the two-dimensional cross DNA nanostructure after assembly.

2. A DNA nanostructure-based logic element according to claim 1, wherein, The sticky end chains in the sticky end group are 6 and uniformly distributed on one side edge of the main body of the two-dimensional cross DNA nanostructure.

3. The DNA nanostructure-based logic element of claim 1, wherein, The capture sequence is a nucleotide sequence added at the 5' end of the DNA staple chain.

4. The DNA nanostructure-based logic element of claim 1, wherein, The label structure is selected from any one of nanogold-mercapto oligonucleotide, streptavidin SA and a fluorescent group.

5. The DNA nanostructure-based logic element of claim 1, wherein, The label structure is SA, the capture sequence is a biotin-modified capture sequence, and the DNA capture chain is a biotin-modified DNA capture chain.

6. The DNA nanostructure-based logic element of claim 1, wherein, The specific sites for capturing the label structure on the two-dimensional cross DNA nanostructure include information sites and check sites, the information sites representing different numbers are arranged above and below the horizontal lines of the cross structure, and the information sites representing different digit numbers are arranged on the left and right sides of the cross structure as high bits and low bits, respectively, and the check sites are arranged on one side of the main body of the two-dimensional cross DNA nanostructure to determine the direction of information reading; correspondingly, 5 capture sequences are arranged on the DNA nanostructure, and one capture sequence captures one label structure.

7. The DNA nanostructure-based logic element of claim 1, wherein, The DNA template chain is the M13mp18 bacteriophage genomic DNA sequence provided in GenBank: X02513.1, and the size of the two-dimensional cross DNA nanostructure is set to 100 nm in length and 100 nm in width.

8. The application of the DNA nanostructure-based logic element in claim 1 in the production of a true random number generator.

9. Use according to claim 8, characterized in that, The application includes the following steps: Step S1, obtaining preset conditions according to the type of random number to be generated, and then producing or selecting different DNA nanostructure-based logic elements according to the preset conditions; including different information represented by the sites and different sticky end groups; The preset condition for obtaining the random number type generated according to the requirement refers to determining the combination times of different numbers according to the bit number of the random number to be generated, and then determining the number of logical elements having a connection relationship, i.e. the value of N in the N-mer, according to the combination times; The different sticky end groups refer to single left setting, single right setting or setting on both sides; the two-dimensional cross DNA nanostructure is matched and connected through the base complementary relationship of the sticky end groups on both sides of the cross paper; In step S2, different DNA nanostructure-based logical elements are mixed in equal proportions, an assembly product is obtained through annealing self-assembly in PCR, SA is added to the assembly product for connection, and a multimer with a marker structure formed is used as a random number generator.

10. Use according to claim 9, characterized in that, The annealing condition is that the starting temperature is 45 DEG C, and the water bath is slowly annealed to the end temperature of 25 DEG C; the obtained annealing product is diluted to 1-2 nM; the obtained diluent is added to SA, and the molar concentration of the site and SA is 1:50.

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