DNA Computing Architecture and Preparation Method Based on Dynamic Assembly of DNA Nanostructures

Abstract

The present invention discloses a DNA computing architecture and a preparation method based on the dynamic assembly of DNA nanostructures, belonging to the field of DNA nanostructures; the architecture includes: a DNA central processing unit, a DNA memory, an input device, and an output device; the DNA central processing unit includes a DNA controller and a DNA arithmetic unit; the DNA controller is a central DNA tetrahedron nanostructure, and the DNA arithmetic unit is an edge DNA tetrahedron nanostructure; the central DNA tetrahedron nanostructure and multiple edge DNA tetrahedron nanostructures form a DNA tetrahedron polymer nanostructure through base complementary pairing of extension strands; the DNA memory is an addressable DNA origami, presenting an asymmetric rectangular two-dimensional DNA nanostructure, including a DNA template strand and a DNA staple strand; capture strands are anchored on the surface of the structure to perform base complementary pairing with the extension strands; and asymmetric DNA origami replacement strands are provided on this structure.

Description

Technical Field

[0001] The present invention belongs to the field of DNA nanostructures, and particularly relates to a DNA computing architecture based on dynamic assembly of DNA nanostructures and a preparation method thereof. Background Art

[0002] Quantum computers have powerful information processing capabilities but lack accuracy and error correction capabilities. Due to the precise base complementary pairing characteristics of DNA molecules, DNA-based biological computers greatly reduce the data error rate. In addition, DNA computing can perform 10^20 operations in parallel, and its computing speed and parallel capabilities far exceed those of silicon-based computers; the physical density of the DNA storage system is 215 PB / g, which is six orders of magnitude higher than that of current storage media. Thanks to the unique advantages of DNA computing and the inherent advantages of DNA such as low cost, easy synthesis, good biocompatibility, and high programmability, DNA computing has received extensive attention and rapid development in recent decades and has become one of the most outstanding candidates for molecular computers.

[0003] Currently, the development of DNA computers mainly focuses on the design and optimization of DNA circuits. A DNA circuit is a molecular information regulation and processing technology and is the basic component for a DNA computer to implement logical operations and logical functions. Logical operations are the basis of molecular computing and are also the basic components of various complex logical devices, playing a crucial role in various multifunctional logical devices. Although DNA circuits based on ssDNA have successfully achieved complex logical operations at the molecular level. However, existing research is still limited to the development of the "arithmetic unit" component in the computer system and has not formed a complete computer structure. In addition, for the logic circuits designed based on ssDNA, electrophoresis technology and fluorescence analysis technology are usually used to monitor the changes in electrophoresis bands and fluorescence intensity to analyze the results of logical operations. The types of operations that can be processed by multiple threads are limited, which restricts the computing power of DNA computers. With the help of single-molecule imaging technology to present the output operation results / information at the single-molecule level, it is expected to achieve multi-threaded operations and outputs in the DNA computing system and improve the computing efficiency. Summary of the Invention

[0004] Aiming at the deficiencies of the prior art, the purpose of the present invention is to provide a DNA computing architecture based on dynamic assembly of DNA nanostructures and a preparation method thereof, which solves the problems in the prior art.

[0005] The purpose of the present invention can be achieved by the following technical solutions:

[0006] A DNA computing architecture based on dynamic assembly of DNA nanostructures includes a DNA central processing unit, a DNA memory, an input device, and an output device; the DNA central processing unit includes a DNA controller and a DNA arithmetic unit;

[0007] The DNA controller is a central DNA tetrahedron nanostructure, and the DNA arithmetic unit is an edge DNA tetrahedron nanostructure; a central DNA tetrahedron nanostructure and multiple edge DNA tetrahedron nanostructures form a DNA tetrahedron polymer nanostructure, namely a DNA central processing unit, through base complementary pairing of extension strands.

[0008] The DNA memory is an addressable DNA origami, presenting an asymmetric rectangular two-dimensional DNA nanostructure, including a DNA template strand and DNA staple strands; multiple capture strands are anchored on the surface of this structure and are respectively base-complementary paired with the extension strands of different edge DNA tetrahedron nanostructures; an asymmetric DNA origami replacement strand is provided on the asymmetric rectangular two-dimensional DNA nanostructure.

[0009] Furthermore, both the central DNA tetrahedron nanostructure and the edge DNA tetrahedron nanostructure are composed of four DNA backbone strands. Each DNA backbone strand folds to form a triangle, constituting each face of the DNA tetrahedron nanostructure. Each edge of the central DNA tetrahedron nanostructure and the edge DNA tetrahedron nanostructure is composed of two DNA strands with base complementary pairing.

[0010] Furthermore, in the DNA tetrahedron polymer nanostructure, the number of edge DNA tetrahedron nanostructures is four; the number of capture strands on the surface of the asymmetric rectangular two-dimensional DNA nanostructure is four and is respectively base-complementary paired with the extension strands of the four edge DNA tetrahedron nanostructures;

[0011] One extension strand is respectively connected to each of the four vertices of the central DNA tetrahedron nanostructure, and one extension strand is respectively connected to one of the vertices of the four edge DNA tetrahedron nanostructures, with a total of 8 extension strands; the four extension strands on the central DNA tetrahedron nanostructure are respectively base-complementary paired with the extension strands on the four edge DNA tetrahedron nanostructures.

[0012] Furthermore, the sequences of the four DNA backbone strands are respectively as shown in SEQ ID NO.1 - SEQ ID NO.4; the sequences of the four extension strands on the four edge DNA tetrahedron nanostructures are respectively as shown in SEQ ID NO.5 - SEQ ID NO.8; the sequences of the four extension strands on the central DNA tetrahedron nanostructure are respectively as shown in SEQ ID NO.9 - SEQ ID NO.12.

[0013] Furthermore, the DNA template strand is the M13mp18 phage genomic DNA sequence; the M13mp18 phage genomic DNA sequence is as shown in SEQ ID NO.13;

[0014] Further, the nucleotide sequences of the four capture strands are shown in SEQ ID NO.32 - SEQ ID NO.35 respectively.

[0015] Further, the nucleotide sequence of the asymmetric DNA origami replacement strand is shown in SEQ ID NO.14 - SEQ ID NO.31.

[0016] The preparation method of the above DNA computing architecture based on the dynamic assembly of DNA nanostructures includes the following steps:

[0017] S1. Mix the DNA template strand, DNA staple strand, asymmetric DNA origami replacement strand, and capture strand in a buffer solution, and obtain an asymmetric rectangular two-dimensional DNA nanostructure through annealing and ultrafiltration purification;

[0018] S2. Mix the DNA backbone strand in a buffer solution, and obtain a central DNA tetrahedron nanostructure and an edge DNA tetrahedron nanostructure with different extension strands through annealing and ultrafiltration purification;

[0019] S3. Mix the central DNA tetrahedron nanostructure and the edge DNA tetrahedron nanostructure in a buffer solution, and obtain a DNA tetrahedron polymer nanostructure through annealing.

[0020] Further, in S1, the buffer solution is 1×TAE / Mg 2+ buffer, in the mixed solution, the concentration of the DNA template strand is 10 nM, and the total concentration of the DNA staple strand, asymmetric DNA origami replacement strand, and DNA capture strand is 80 nM;

[0021] The buffer solutions in S2 and S3 are TM buffer; and in S3, the five DNA tetrahedron nanostructures are in an equimolar ratio.

[0022] The application of the above DNA computing architecture based on the dynamic assembly of DNA nanostructures in miRNA detection.

[0023] The beneficial effects of the present invention:

[0024] (1) The present invention uses a simpler and more effective system based on the strand displacement method to achieve the dynamic conversion of DNA nanostructures;

[0025] (2) The present invention provides a construction method and application of a DNA computing system based on dynamic DNA nanostructures. Using DNA nanostructures as computing modules of the DNA computing architecture, the designed DNA nanostructures have uniform sizes, the programmable sites for recombination provide precise node site designs, and the rich extensible side chains can provide stable and reliable physical connection relationships;

[0026] (3)The present invention provides a method for constructing a DNA computing system based on dynamic DNA nanostructures and its application, which also has the function of detecting multiple miRNAs. The DNA fuel strand used is a DNA strand equivalent to miRNA. The present invention can also efficiently and simply detect multiple miRNAs.

[0027] (4)The asymmetric rectangular two-dimensional DNA nanostructure and DNA tetrahedron nanostructure mainly used in the present invention have good biocompatibility, and other required chemical and biological materials are also non-toxic to the human body. BRIEF DESCRIPTION OF THE DRAWINGS

[0028] In order to more clearly illustrate the technical solutions in the embodiments of the present invention or the prior art, the following will briefly introduce the drawings required for the description of the embodiments or the prior art. Obviously, for those of ordinary skill in the art, without creative efforts, other drawings can also be obtained based on these drawings.

[0029] Figure 1 It is the operation flowchart of the DNA computing system based on the dynamic assembly of DNA nanostructures of the present invention;

[0030] Figure 2 It is the schematic diagram of node information encoding in the present invention;

[0031] Figure 3 It is the PAGE experimental result diagram of the DNA arithmetic unit and DNA controller in the present invention;

[0032] Figure 4 It is the PAGE experimental result diagram of the DNA central processing unit in the present invention;

[0033] Figure 5 It is the morphological characterization diagram of the DNA central processing unit in the present invention;

[0034] Figure 6 For Figure 5 The enlarged schematic diagram at position A in

[0035] Figure 7 It is the morphological characterization diagram of the DNA memory in the present invention;

[0036] Figure 8 It is the PAGE experimental result diagram of the operation process in the present invention;

[0037] Figure 9 It is the morphological characterization diagram of the operation result in the present invention. DETAILED DESCRIPTION OF THE INVENTION

[0038] The technical solutions in the embodiments of the present invention will be clearly and completely described below with reference to the accompanying drawings in the embodiments of the present invention. Obviously, the described embodiments are only a part of the embodiments of the present invention, rather than all the embodiments. All other embodiments obtained by those of ordinary skill in the art based on the embodiments of the present invention without creative efforts shall fall within the protection scope of the present invention.

[0039] Embodiment 1

[0040] A DNA computing architecture based on the dynamic assembly of DNA nanostructures includes a DNA central processing unit module, a DNA memory module, an input device, and an output device; the DNA central processing unit module includes a DNA controller and a DNA arithmetic unit.

[0041] The DNA central processing unit module is a DNA tetrahedron multimer nanostructure that dynamically responds to input information; the DNA controller is the central DNA tetrahedron nanostructure in the DNA tetrahedron multimer nanostructure; the DNA arithmetic unit is four edge DNA tetrahedron nanostructures connected to the central DNA tetrahedron nanostructure; the DNA tetrahedron multimer nanostructure (DNA central processing unit module) is composed of a central DNA tetrahedron nanostructure (DNA controller) and four edge DNA tetrahedron nanostructures (DNA arithmetic units) through base complementary pairing of extension strands.

[0042] In this embodiment, both the central DNA tetrahedron nanostructure and the edge DNA tetrahedron nanostructure are composed of four DNA backbone strands. Each DNA backbone strand folds to form a triangle, constituting each face of the DNA tetrahedron nanostructure. Each edge of the DNA tetrahedron nanostructure is composed of two DNA strands with base complementary pairing. Moreover, one extension strand is respectively connected to each of the four vertices of the central DNA tetrahedron nanostructure, and one extension strand is respectively connected to one of the vertices of the four edge DNA tetrahedron nanostructures, totaling 8 extension strands; the four extension strands on the central DNA tetrahedron nanostructure are respectively base complementary paired with the extension strands on the four edge DNA tetrahedron nanostructures.

[0043] The sequences of the four DNA backbone strands constituting the DNA tetrahedron nanostructure are respectively as shown in SEQ ID NO.1 - SEQ ID NO.4; the sequences of the four extension strands on the four edge DNA tetrahedron nanostructures (DNA arithmetic units) are respectively as shown in SEQ ID NO.5 - SEQ ID NO.8; the sequences of the four extension strands on the central DNA tetrahedron nanostructure (DNA controller) are respectively as shown in SEQ ID NO.9 - SEQ ID NO.12.

[0044] The DNA memory module is an addressable DNA origami, which is an asymmetric rectangular two-dimensional DNA nanostructure that includes a DNA template strand and DNA staple strands; the DNA template strand is the M13mp18 phage genomic DNA sequence; the M13mp18 phage genomic DNA sequence is as shown in SEQ ID NO.13;

[0045] Among them, the asymmetric rectangular two-dimensional DNA nanostructure replaces and adds a part of the DNA staple strands to form an asymmetric DNA origami replacement strand, so that the rectangular two-dimensional DNA nanostructure has asymmetry. The nucleotide sequences of the replacement and addition of the asymmetric rectangular two-dimensional DNA nanostructure (i.e., the asymmetric DNA origami replacement strand) are as shown in SEQ ID NO.14 - SEQ ID NO.31;

[0046] Four capture strands are anchored on the surface of the asymmetric rectangular two-dimensional DNA. The sequence of each capture strand is base complementary paired with the extended strand sequence of the DNA tetrahedron nanostructure (edge DNA tetrahedron nanostructure). Each capture strand captures one DNA tetrahedron nanostructure; the nucleotide sequences of the four capture strands are as shown in SEQ ID NO.32 - SEQ ID NO.35 respectively.

[0047] The input device is implemented by an instruction DNA strand, which is a single-stranded structure and can also be called a DNA fuel strand. Based on strand displacement, in the catalytic DNA computing architecture, the input DNA fuel strand can be recycled multiple times. The input DNA fuel strand can directly react with the reaction system to produce output products. It maintains its own computing function without being consumed in the reaction system.

[0048] In this embodiment, the nucleotide sequence of the instruction DNA strand is as shown in SEQ ID NO.36 - SEQ ID NO.39.

[0049] Example 2

[0050] In this embodiment, a preparation method of a DNA computing architecture based on the dynamic assembly of DNA nanostructures is proposed, and the raw materials and reagents involved in the preparation process are described as follows:

[0051] 1. Tris(hydroxymethyl)aminomethane (Tris), disodium ethylenediaminetetraacetate (EDTA), magnesium acetate, glacial acetic acid, and boric acid are all purchased from Sinopharm Chemical Reagent Co., Ltd.; the experimental water is all ultrapure water.

[0052] 2. 30 kDa and 100 kDa ultrafiltration tubes are purchased from Pall China.

[0053] 3. The genomic DNA of M13mp18 phage was purchased from BioHite Biotechnology Co., Ltd., with the product number and specification being B3003-50 pmol; both the DNA template strand and the DNA staple strand were purchased from Shanghai Sangon Biotech Co., Ltd.; the DNA backbone strand, the instruction DNA strand, and the capture strand were all purchased from GenScript Biotech Corporation.

[0054] 4. The stock solution used in the polyacrylamide gel electrophoresis (PAGE) experiment was a 30% acrylamide / N,N'-methylenebisacrylamide (Acr / Bis) solution, purchased from Shanghai Sangon Biotech Co., Ltd.

[0055] The experimental reaction of Example 2 was carried out in 1×TAE-Mg 2+ buffer (40 mM Tris, 20 mM glacial acetic acid,

[0056] 2 mM EDTA and 12.5 mM magnesium acetate tetrahydrate, pH = 8.0) and TM buffer (10 mM Tris, 5 mM magnesium chloride hexahydrate, pH = 8.0).

[0057] The detection method for the polyacrylamide gel electrophoresis (PAGE) experiment: Prepare an 8% PAGE gel (3.8 L ultrapure water, 1 mL stock solution, 80 μL 10% ammonium persulfate (APS) solution, 8 μL N,N,N',N'-tetramethylethylenediamine (TEMED) solution). Prepare a 5% PAGE gel (4.4 mL distilled water, 1 mL 30% PAGE solution, 100 μL 10% ammonium persulfate (APS) solution, 6 μL N,N,N',N'-tetramethylethylenediamine (TEMED) solution).

[0058] For those not specifying specific techniques or conditions in the examples, they are carried out according to the techniques or conditions described in the literature in this field or according to the product instructions. For reagents or instruments without indicating the manufacturer, they are all conventional products that can be obtained through regular channels.

[0059] A preparation method for the DNA computing system architecture based on the dynamic assembly of DNA nanostructures includes the following steps:

[0060] S1, prepare a DNA central processor;

[0061] Mix the four DNA backbone strands for constructing the tetrahedral nanostructure. The sequences of the DNA backbone strands of the four DNA tetrahedral nanostructures are shown in SEQ ID NO.1 - SEQ ID NO.4 respectively, and the sequences of the extension strands of the DNA tetrahedral nanostructures are shown in SEQ ID NO.5 - SEQ ID NO.12 respectively. Among them, the DNA controller and the DNA arithmetic unit use DNA strands with different extension strands to synthesize the DNA tetrahedral nanostructure, and the final concentration of the DNA tetrahedral nanostructure is set to 1000 nM.

[0062] 2) Use a PCR instrument to anneal the mixed DNA backbone strands. The annealing conditions are: temperature 95 °C, hold for 10 min, then cool to 4 °C and hold for 20 min to obtain different DNA tetrahedral nanostructures.

[0063] 3) After the annealing program ends, take out the DNA tetrahedral nanostructure and separate it using a 30 kDa ultrafiltration tube to remove the un-synthesized DNA backbone strands. The centrifugation conditions are: add 300 μL of TM buffer to 100 μL of the sample, centrifuge at 3000 rcf / min for 10 min, and repeat the centrifugation 3 times. Finally, put the collected DNA tetrahedral nanostructures into different centrifuge tubes. Then use ultraviolet spectroscopy to quantify the DNA tetrahedral nanostructure.

[0064] Verify the tetrahedron synthesis effect through PAGE experiment, as Figure 3 shown. Lane 1: DNA molecular weight standard Marker (25 - 500 bp); Lane 2: 1 nucleotide chain constituting the DNA tetrahedral nanostructure; Lane 3: Formed by the pairing of 2 nucleotide chains constituting the DNA tetrahedron; Lane 4: Formed by the pairing of 3 nucleotide chains constituting the DNA tetrahedron; Lane 5: Formed by the pairing of 4 nucleotide chains constituting the DNA tetrahedron, that is, the DNA tetrahedral nanostructure without extension strands; Lanes 6 - 9: DNA tetrahedron with one different extension strand, that is, the DNA arithmetic unit; Lane 10: DNA tetrahedral nanostructure with 4 different extension strands, that is, the DNA controller.

[0065] 4) Add five DNA tetrahedral nanostructures (one central DNA tetrahedral nanostructure and four peripheral DNA tetrahedral nanostructures) into a centrifuge tube according to the molar ratio of 1:1:1:1:1 at the unit point. The annealing conditions are: hold at 37 °C for 2 h, and its structural concentration is set to 250 nM.

[0066] Verify the synthesis effect of the DNA tetrahedral polyhedral nanostructure, that is, the DNA central processor, through PAGE experiment, as Figure 4As shown in the figure. Lane 1: DNA molecular weight standard Marker (100 - 1200 bp); Lanes 2 - 5: Four DNA tetrahedron nanostructures with one different extended strand, namely DNA arithmetic units; Lane 6: DNA tetrahedron nanostructure with four different extended strands, namely DNA controller; Lanes 7 - 10: DNA tetrahedron dimer nanostructures formed by pairwise connection of DNA controller and DNA arithmetic unit; Lane 11: DNA tetrahedron polymer nanostructure, namely DNA central processor structure.

[0067] The synthesis effect of the DNA tetrahedron polymer nanostructure, namely DNA central processor, was verified by atomic force microscopy experiments. As Figure 5 and Figure 6 shown, it can be seen that this structure has five DNA tetrahedron nanostructures, and from the image, it can also be seen that its synthesis effect is consistent with the expected designed structure.

[0068] S2, construct a DNA memory module;

[0069] The preparation raw materials include: M13mp18 template strand shown in SEQ ID NO.13 and DNA short strands. The DNA short strands include: DNA staple strands with 180 sequences, 18 asymmetric DNA origami replacement strands shown in SEQ ID NO.14 - SEQ ID NO.31 (to make the rectangular two-dimensional DNA nanostructure have asymmetry), and 4 DNA capture strands shown in SEQ ID NO.32 - SEQ ID NO.35.

[0070] Among them, the 180 sequences of DNA staple strands are selected from the "Supporting information" of "Shen, C; Lan, X; Lu, X; Ni, W; Wang, Q. Tuning the structural asymmetries of three-dimensional gold nanorod assemblies. Chemical Communications 2015, 51 (71), 13627 - 13629.", specifically, the remaining 180 sequences after removing sequences 25, 60, 70, 113, 133, 135, 157, 159, 162, 174, 181, 183 from sequences 1 - 99 and 112 - 204 in the "Sequence of staple strands used in the assembly of basic rectangular DNA origami (left to right 5’ - 3’)" disclosed in the above literature.

[0071] 1) Mix the above DNA strands in 1×TAE / Mg 2+ buffer. The total volume after mixing is 100 μL, where the concentration of the M13mp18 template strand is 10 nM, equal amounts and in excess of each DNA short strand sequence are added, and the total concentration of the DNA short strands is 80 nM;

[0072] 2) Slowly anneal the mixture of the above M13mp18 template strand and DNA short strands using a gradient PCR instrument. The annealing conditions are: starting temperature 95 °C, holding for 3 min, ending temperature 25 °C, with a gradient of 1 °C each, staying at each gradient for 100 s, annealing from 95 °C to 25 °C within two hours,

[0073] 3) Take out the sample and centrifuge it using a 100 kDa centrifuge tube to remove the excess DNA short strands; the centrifugation conditions are: add 300 μL of 1×TAE-Mg 2+ buffer to 100 μL of the sample, and centrifuge at 3000 rcf / min for 10 min, repeating the centrifugation 3 times;

[0074] Finally, observe the morphology of the lamellar structure of the collected sample using an atomic force microscope (AFM). The results are as Figure 7 shown. The constructed DNA nanostructure is in a rectangular lamellar structure. The AFM characterization results show that the rectangular two-dimensional DNA nanostructure is about 90 nm long and about 60 nm wide, and has asymmetry.

[0075] Example 3

[0076] In this example, the application of a DNA computing system in dynamic operations in a simulated von Neumann architecture is disclosed;

[0077] The operation process of the DNA arithmetic unit is run through DNA strand displacement; four edge DNA tetrahedron nanostructures are connected to the central DNA tetrahedron nanostructure through base complementary pairing, and the four strands extending from the central DNA tetrahedron nanostructure have four different DNA strand displacement footholds.

[0078] As Figure 2 shown, obtain preset conditions according to the item to be operated, and encode the capture sites of the asymmetric rectangular two-dimensional DNA nanostructure according to the preset conditions; the preset conditions include the number of edge DNA tetrahedron nanostructures, i.e., the number of DNA arithmetic units, the connection between the central DNA tetrahedron nanostructure and the edge DNA tetrahedron nanostructures, and the sequence and number of the instruction DNA strands, i.e., DNA fuel strands.

[0079] As Figure 1As shown, the DNA nanostructure module constructed according to preset conditions (the DNA tetrahedron multimer nanostructure, i.e., the DNA central processor), the instruction DNA strand, and the DNA memory are mixed and annealed in the DNA computing architecture, diluted to a certain concentration, and then detected using a detector to obtain the operation result.

[0080] The annealing conditions are as follows: the starting temperature is 45 °C, the ending temperature is 25 °C, with a gradient of 1 °C each, and each gradient stays for 5 minutes, for 5 cycles. The molar ratio of the instruction DNA strand to the DNA nanostructure module (the DNA tetrahedron multimer nanostructure, i.e., the DNA central processor) is 10:1; the instruction DNA strand is as shown in SEQ ID NO.36 - SEQ ID NO.39.

[0081] The PAGE experiment is used to verify the operation process effect of the DNA arithmetic unit, as Figure 8 shown. Lane 1: DNA molecular weight standard Marker (100 - 1200 bp); Lane 2: the pentamer high-order DNA nanostructure of the DNA tetrahedron, i.e., the DNA central processor; Lanes 3 - 6: the operation results with 1 replacement strand added according to the preset conditions; Lanes 7 - 12: the operation results with 2 replacement strands added according to the preset conditions; Lane 13: DNA molecular weight standard Marker (100 - 1200 bp); Lane 14: the pentamer high-order DNA nanostructure of the DNA tetrahedron, i.e., the DNA central processor as a control; Lanes 15 - 19: the operation results with 3 replacement strands added according to the preset conditions; Lane 19: the operation results with 4 replacement strands added according to the preset conditions; Lane 20: the DNA tetrahedron nanostructure with 4 different extended strands, i.e., the DNA controller as a control group; Lanes 21 - 24: four DNA tetrahedron nanostructures with 1 different extended strand, i.e., the DNA arithmetic units as control groups.

[0082] The atomic force microscope experiment is used to verify the output of different operation results and is presented in the form of a Karnaugh map, as Figure 9 shown. It can be seen that this DNA computing architecture can operate successfully, which is consistent with Figure 2 the designed operation result display effect.

[0083] In the description of this specification, the descriptions referring to terms such as "one embodiment", "example", "specific example", etc. mean that the specific features, structures, materials, or characteristics described in connection with the embodiment or example are included in at least one embodiment or example of the present invention. In this specification, the schematic representations of the above terms do not necessarily refer to the same embodiment or example. Moreover, the specific features, structures, materials, or characteristics described can be combined in a suitable manner in any one or more embodiments or examples.

[0084] The foregoing has shown and described the basic principles, main features and advantages of the present invention. Those skilled in the art should understand that the present invention is not limited by the above embodiments, and what is described in the above embodiments and the specification is only to illustrate the principles of the present invention. Without departing from the spirit and scope of the present invention, the present invention will have various changes and improvements, and these changes and improvements fall within the scope of the present invention claimed.

Claims

1. A DNA computing architecture based on dynamic assembly of DNA nanostructures, characterized in that: It includes a DNA central processor, a DNA memory, an input device and an output device; the DNA central processor includes a DNA controller and a DNA operator; The DNA controller is a central DNA tetrahedron nanostructure, and the DNA operator is an edge DNA tetrahedron nanostructure; a central DNA tetrahedron nanostructure and a plurality of edge DNA tetrahedron nanostructures form a DNA tetrahedron polymer nanostructure through complementary pairing of extended chain bases, i.e., a DNA central processor; The DNA memory is an addressable DNA origami in the form of an asymmetric rectangular two-dimensional DNA nanostructure, comprising a DNA template chain and a DNA staple chain; a plurality of capture chains are anchored on the surface of the asymmetric rectangular two-dimensional DNA nanostructure, and are respectively complementary to the extended chains of different edge DNA tetrahedral nanostructures in base pairing; an asymmetric DNA origami replacement chain is arranged on the asymmetric rectangular two-dimensional DNA nanostructure.

2. The DNA computing architecture based on dynamic assembly of DNA nanostructures according to claim 1, characterized in that: The central DNA tetrahedron nanostructure and the edge DNA tetrahedron nanostructure are both composed of four DNA backbone chains, each of which is stacked to form a triangle to form each face of the DNA tetrahedron nanostructure, and each side of the central DNA tetrahedron nanostructure and the edge DNA tetrahedron nanostructure is composed of two DNA chains with complementary base pairing.

3. The DNA computing architecture based on dynamic assembly of DNA nanostructures according to claim 2, characterized in that: In the DNA tetrahedral polymer nanostructure, the number of edge DNA tetrahedral nanostructures is four; the number of capture chains on the surface of the asymmetric rectangular two-dimensional DNA nanostructure is four, and they are respectively complementary to the extended chains of the four edge DNA tetrahedral nanostructures; The four vertices of the central DNA tetrahedron nanostructure are respectively connected to an extended chain, and one of the vertices of the four edge DNA tetrahedron nanostructures is respectively connected to an extended chain, with a total of 8 extended chains; the four extended chains on the central DNA tetrahedron nanostructure are respectively complementary to the extended chains on the four edge DNA tetrahedron nanostructures in base pairing.

4. The DNA computing architecture based on dynamic assembly of DNA nanostructures according to claim 3, characterized in that: The sequences of the four DNA backbone chains are shown as: SEQ ID NO.1-SEQ ID NO.4; The sequences of the four extended chains on the four edge tetrahedral DNA nanostructures are shown as SEQ ID NO.5 to SEQ ID NO.8 respectively; the sequences of the four extended chains on the central tetrahedral DNA nanostructure are shown as SEQ ID NO.9 to SEQ ID NO.12 respectively.

5. The DNA computing architecture based on dynamic assembly of DNA nanostructures according to claim 2, characterized in that: The DNA template strand is the M13mp18 phage genomic DNA sequence; the M13mp18 phage genomic DNA sequence is shown as SEQ ID NO.

13.

6. The DNA computing architecture based on dynamic assembly of DNA nanostructures according to claim 3, characterized in that: The nucleotide sequences of the four capture chains are shown in SEQ ID NO.32 to SEQ ID NO.35 respectively.

7. The DNA computing architecture based on dynamic assembly of DNA nanostructures according to claim 2, characterized in that: The nucleotide sequences of the asymmetric DNA origami replacement chains are shown in SEQ ID NO.14 to SEQ ID NO.

31.

8. The method for preparing a DNA computing architecture based on dynamic assembly of DNA nanostructures according to any one of claims 2 to 7, characterized in that: The following steps are involved: S1, the DNA template strand, DNA staple strand, asymmetric DNA origami replacement strand and capture strand are mixed in a buffer solution, and an asymmetric rectangular two-dimensional DNA nanostructure is obtained after annealing and ultrafiltration purification; S2, mixing the DNA backbone chains in a buffer, annealing, and ultrafiltration purification to obtain central DNA tetrahedral nanostructures and edge DNA tetrahedral nanostructures with different extended chains; S3, mixing the central DNA tetrahedral nanostructure and the edge DNA tetrahedral nanostructure in a buffer solution, and annealing to obtain a DNA tetrahedral polymer nanostructure.

9. The method for preparing a DNA computing architecture based on dynamic assembly of DNA nanostructures according to claim 8, characterized in that: In S1, the buffer is 1×TAE / Mg 2+ buffer, in the mixed solution, the concentration of the DNA template strand was 10 nM, and the total concentration of the DNA staple strand, the asymmetric DNA origami replacement strand, and the capture strand was 80 nM; The buffer in S2 and S3 is TM buffer.

10. Application of the DNA computing architecture based on dynamic assembly of DNA nanostructures according to any one of claims 1 to 7 in miRNA detection.

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