Molecular system based on DNA nano-structure artificial atoms and construction and regulation method

Abstract

The invention discloses a molecular system based on DNA nano-structure artificial atoms and a construction and regulation method, and belongs to the technical field of DNA nanotechnology. The construction method of the molecular system comprises the following steps: mixing DNA chains with extension chains, adding a TM buffer solution, and carrying out annealing reaction to synthesize a DNA nano-structure with extension chains; dNA nanostructures are used for representing artificial atoms, extended chains on the DNA nanostructures are used for representing valence electrons, double chains formed by interaction among the extended chains are used for representing chemical bonds, a plurality of DNA nanostructures with extended chains are mixed in proportion according to a target molecular configuration, and a molecular system is obtained through one-pot assembly. Dynamic dissociation and recombination of artificial atoms are achieved based on DNA strand displacement reaction, and accurate regulation and control of a programmable molecular system are achieved. The construction precision and regulation effectiveness of the molecular system are verified through various technologies, the system has the advantages of being high in programmability, high in assembly efficiency, good in structural controllability and the like, and a brand new technical platform is provided for the fields of material design, chemical process simulation, biological engineering and the like.

Description

Technical Field

[0001] This invention belongs to the field of DNA nanotechnology, specifically relating to molecular systems based on DNA nanostructured artificial atoms and their construction and regulation methods. Background Technology

[0002] Artificial atoms are nanoscale model systems that simulate the behavior of real atoms and molecules, and they are of great significance in the construction of complex nanostructures and the development of novel materials. However, traditional artificial atom-based materials suffer from problems such as poor programmability, low assembly precision, and difficulty in functional control, which limit their application in molecular simulation and precise control.

[0003] The rise of DNA nanotechnology has provided entirely new avenues for the development of artificial atoms. DNA molecules, as carriers of genetic information, possess a unique double helix structure and the strict Watson-Crick base pairing rule, giving them inherent programmability. By designing base sequences, the pairing patterns and assembly morphology of DNA molecules can be precisely controlled. Furthermore, the size of DNA molecules can be precisely controlled at the nanoscale, and they exhibit excellent biocompatibility and structural stability. These properties make them ideal materials for the field of molecular self-assembly.

[0004] For many years, researchers have used DNA self-assembly to directly or indirectly construct a wide variety of sophisticated nanostructures. In this process, DNA tiles, DNA origami, DNA bricks, and framework nucleic acids are often used as basic structural units to achieve precise manipulation and construction of complex structures. Using various DNA nanostructures as artificial atoms offers several significant advantages: First, DNA nanostructures are highly programmable, allowing for precise design of base sequences to flexibly control the size, configuration, and surface modification sites of the nanostructures, adapting to the simulation needs of different element atoms; second, DNA nanostructures have high assembly precision, based on the Watson-Crick base pairing principle, enabling atomic-level positioning and connection, ensuring the accuracy of molecular system construction; third, DNA nanostructures exhibit excellent stability, with the inherent chemical stability of DNA molecules and the framework structure formed by self-assembly maintaining morphological integrity under various reaction conditions; fourth, DNA nanostructures also have strong functional extensibility, allowing for the modification of functional units such as extended chains and fluorescent groups at specific sites to achieve diverse functions such as valence bond simulation and signal detection; and finally, DNA nanostructures have good biocompatibility, no toxic side effects, and are suitable for fields such as biomedicine where material safety is paramount.

[0005] Simulating the structure of natural molecules allows for a deeper understanding of their structure and function, and can also inspire and promote the design and development of new materials. Therefore, developing a method for constructing and controlling programmable molecular systems that is universal, precise, and dynamically controllable, to address the limitations and inaccuracies in the dynamic control of artificial atoms, has become a key research direction in the field of DNA nanotechnology. Summary of the Invention

[0006] In view of the shortcomings of the prior art, the purpose of this invention is to provide a molecular system based on DNA nanostructure artificial atoms and a method for its construction and regulation, thereby solving the problems in the prior art.

[0007] The objective of this invention can be achieved through the following technical solutions: The method for constructing molecular systems based on DNA nanostructured artificial atoms includes the following steps: DNA strands with extended strands are mixed, added to TM buffer solution, and then annealed to synthesize DNA nanostructures with extended strands. Artificial atoms are represented by DNA nanostructures, valence electrons are represented by the extended strands on the DNA nanostructures, and chemical bonds are represented by the double strands formed by the interaction between the extended strands. According to the target molecular configuration, multiple DNA nanostructures with extended strands are mixed in proportion and assembled into a molecular system through a one-pot method.

[0008] Furthermore, the DNA nanostructure is: a DNA tetrahedron, a DNA cube, a DNA octahedron, or any three-dimensional nanostructure constructed using DNA origami technology.

[0009] Furthermore, the annealing process is as follows: hold at 95°C for 10 minutes, then cool down to 4°C and hold for 20 minutes.

[0010] Furthermore, the DNA strand with the extended strand includes: DNA strands as shown in SEQ ID NO:33~78.

[0011] Furthermore, the molecular system includes one or more of the following: linear structure, cyclic structure, branched structure, two-dimensional network structure, or three-dimensional spatial structure.

[0012] A programmable molecular system is constructed using the above-described construction method.

[0013] The above-mentioned programmable molecular systems are used in simulating chemical reactions.

[0014] The method for simulating chemical reactions using the above-mentioned programmable molecular system includes the following steps: After mixing the programmable molecular system with the substitution chain, the reaction is carried out by heating in a water bath, and the mixture dissociates to form an intermediate. DNA nanostructures with extended strands are mixed with intermediates and self-assembled by heating in a water bath to form new molecular systems.

[0015] The above-mentioned method for dynamic control of programmable molecular systems includes the following steps: In a solution environment, the molecular system is mixed with the bridging chain and reacted by heating in a water bath, so that the bridging chain and the extended chain in the molecular system are partially complementary, thereby achieving the combination of double chains. An excess of substitutional chain is added to the molecular system after the bridging chain is combined, and the reaction is carried out by heating in a water bath. The substitutional chain combines with the double chain and replaces the original bridging chain, thus restoring the configuration of the molecular system.

[0016] Furthermore, the bridging chain sequence is shown in SEQ ID NO:79-80, and the substitution chain sequence is shown in SEQ ID NO:81-82.

[0017] The beneficial effects of this invention are: 1. This invention can accurately simulate the atomic, chemical valence bond and organic molecular structure of different elements by designing DNA nanostructures of different sizes, the number of extended strands and sequences. Theoretically, it can construct any organic molecular system and has strong programmability.

[0018] 2. Based on the Watson-Crick base pairing principle, the assembly error of artificial atoms in DNA nanostructures is controlled at the nanoscale. The high structure assembly yield is verified by AFM characterization.

[0019] 3. This invention provides a simpler and more effective regulation method based on strand substitution, which realizes the dissociation and recombination of molecular structures through DNA strand substitution reaction, realizes the dynamic regulation process of molecular systems, simulates the movement process of bacterial flagella motors, reveals the dynamic movement mechanism at the molecular scale, elucidates the mechanical movement driven by non-covalent interactions (base pairing, conformational changes), and provides a simplified biomimetic model for understanding the molecular dynamics behavior in life processes.

[0020] 4. The DNA nanostructures primarily used in this invention possess excellent biocompatibility, and the other required chemical and biological materials are also non-toxic to humans, making it suitable for multiple fields such as new material development and research on chemical reaction mechanisms. Attached Figure Description

[0021] To more clearly illustrate the technical solutions in the embodiments of the present invention or the prior art, the drawings used in the description of the embodiments or the prior art will be briefly introduced below. Obviously, for those skilled in the art, other drawings can be obtained based on these drawings without creative effort.

[0022] Figure 1These are morphological characterization diagrams of DNA tetrahedral artificial atoms of different sizes used in this invention. Figure 2 The image shows the PAGE experimental results of DNA tetrahedra of different sizes in this invention. Figure 3 This is a morphological characterization diagram of the hydrocarbon molecular system constructed using DNA tetrahedra in this invention; Figure 4 This is a morphological characterization diagram of the molecular system of hydrocarbon derivatives constructed using DNA tetrahedra in this invention. Figure 5 This is a morphological characterization diagram of the molecular system constructed using DNA tetrahedra to simulate chemical reactions in this invention; Figure 6 This is a morphological characterization diagram of the molecular system constructed using DNA tetrahedra in this invention; Figure 7 This is a morphological characterization diagram of the molecular system for dynamic regulation in this invention. Detailed Implementation

[0023] The technical solutions of the embodiments of the present invention will be clearly and completely described below with reference to the accompanying drawings. Obviously, the described embodiments are only some embodiments of the present invention, and not all embodiments. Based on the embodiments of the present invention, all other embodiments obtained by those skilled in the art without creative effort are within the scope of protection of the present invention.

[0024] Where specific techniques or conditions are not specified in the examples, they shall be performed in accordance with the techniques or conditions described in the literature in this field, or in accordance with the product instructions. Reagents or instruments whose manufacturers are not specified are all conventional products that can be purchased through legitimate channels.

[0025] The following description of the raw materials and reagents used in the preparation process and examples. 1. Tris(hydroxymethyl)aminomethane (Tris), disodium EDTA dihydrate (C 10 H 14 N2O8Na2·2H2O), acetic acid (CH3COOH), magnesium acetate tetrahydrate (Mg(CH3COO)2·4H2O), boric acid (H3BO3), ammonium persulfate ((NH4)2S2O8), tetramethylethylenediamine (C6H 16 N2) was purchased from Shanghai Sinopharm Chemical Reagent Co., Ltd.; 3-aminopropyltriethoxysilane (H2NCH2CH2CH2Si(OC2H5)3) was purchased from Cool Chemical Technology (Beijing) Co., Ltd.; ultrafiltration tubes (molecular weight cutoff of 30kDa) were purchased from Merck, Inc.; gel DNA extraction centrifuge column was purchased from Bio-Rad; and all experimental water was ultrapure water.

[0026] 2. The DNA strands, bridging strands, and substitution strands were purchased from Genscript Biotech Inc., and their sequences are shown in SEQ ID NO: 1~82.

[0027] 3. The stock solution used in the polyacrylamide gel electrophoresis (PAGE) experiment was a 30% PAGE solution, purchased from Shanghai Sangon Biotech Co., Ltd.

[0028] The experimental reactions in the examples were performed in 1×TM buffer (10 mM Tris, 5 mM MgCl2, final solution pH = 8.0), 10×TAE-Mg 2+ Solution (200 mM CH3COOH, 400 mM Tris, 20 mM EDTA-2Na, 125 mM Mg(CH3COO)2·4H2O, pH value approximately 8.0), 5×TBE solution (450 mM H3BO3, 450 mM Tris, 10 mM EDTA-2Na, pH value approximately 8.0).

[0029] Polyacrylamide gel electrophoresis (PAGE) assay method: Prepare 8% PAGE gel (3.8 mL ultrapure water, 1.6 mL 30% PAGE solution, 0.6 mL 10×TAE-Mg). 2+ Solution: 80 μL 10% ammonium persulfate (APS) solution, 8 μL tetramethylethylenediamine (TEMED) solution. Prepare 6% PAGE gel (4.2 mL ultrapure water, 1.2 mL 30% PAGE solution, 0.6 mL 10×TAE-Mg). 2+ Solution: 100 μL 10% ammonium persulfate (APS) solution, 6 μL tetramethylethylenediamine (TEMED) solution. Prepare 5% PAGE gel (4.4 mL ultrapure water, 1 mL 30% PAGE solution, 0.6 mL 10×TAE-Mg). 2+ The solution consisted of 100 μL of 10% ammonium persulfate (APS) solution and 6 μL of tetramethylethylenediamine (TEMED) solution.

[0030] Agarose gel electrophoresis (AGE) assay method: Prepare 1% agarose gel (0.4 g agarose, 40 mL 0.5×TBE solution).

[0031] Where specific techniques or conditions are not specified in the examples, they shall be performed in accordance with the techniques or conditions described in the literature in this field, or in accordance with the product instructions. Reagents or instruments whose manufacturers are not specified are all conventional products obtainable through legitimate channels.

[0032] To achieve the above-mentioned objectives, the present invention provides the following technical solution: Example 1 In this embodiment, DNA tetrahedra of different sizes are synthesized to construct artificial atoms. First, equimolar amounts of DNA strands composing the DNA tetrahedra were mixed. Different sized DNA tetrahedra were composed of DNA strands of varying lengths. TM buffer was added to achieve a final concentration of 1 μM and a final volume of 100 μL. The sample was then placed in a PCR instrument for annealing. The annealing program was 95 °C for 10 minutes, followed by rapid cooling to 4 °C and incubation for 20 minutes. After annealing and assembly, the DNA tetrahedra were placed in an ultrafiltration tube with a molecular weight cutoff of 30 kDa and centrifuged at 3000 g for 10 minutes. This process was repeated three times for ultrafiltration purification to remove incompletely assembled DNA strands, thereby recovering the high-purity DNA tetrahedral structure. The concentration of the DNA tetrahedra was determined using an ultra-micro spectrophotometer. The DNA strand sequences are shown in SEQ ID NO:1-32.

[0033] The DNA tetrahedrons of different sizes and their corresponding elements are as follows: the DNA tetrahedron with a side length of 13 bp corresponds to boron (B), the DNA tetrahedron with a side length of 20 bp corresponds to carbon (C), the DNA tetrahedron with a side length of 26 bp corresponds to nitrogen (N), the DNA tetrahedron with a side length of 30 bp corresponds to oxygen (O), and the DNA tetrahedron with a side length of 37 bp corresponds to chlorine (Cl).

[0034] The synthesis efficiency of DNA tetrahedra of different sizes was verified using atomic force microscopy experiments. Figure 1 ).

[0035] The synthesis effect of tetrahedra of different sizes was verified by 5% polyacrylamide gel electrophoresis. Figure 2 Lane 1: DNA molecular weight standard marker (25-500 bp); Lanes 2-6 represent DNA tetrahedra of boron (B), carbon (C), nitrogen (N), oxygen (O), and chlorine (Cl), respectively.

[0036] Example 2 In this embodiment, a variety of hydrocarbon molecular systems are constructed using DNA tetrahedra with a side length of 20 bp as artificial atoms; 1. Functional modification of DNA tetrahedral artificial atoms with a side length of 20 bp Equimolar amounts of DNA strands with extended strands were mixed and TM buffer was added to synthesize DNA tetrahedra with extended strands to a final concentration of 1 μM and a final volume of 100 μL. The samples were then placed in a PCR instrument for annealing. The annealing program was 95 °C for 10 minutes, followed by rapid cooling to 4 °C and incubation for 20 minutes. After annealing and assembly, DNA tetrahedra with one, two, three, or four extended strands were synthesized. Depending on the molecular conformation, the number and type of extended strands in the DNA tetrahedra varied. The samples were then placed in ultrafiltration tubes with a molecular weight cutoff of 30 kDa for ultrafiltration purification, thereby recovering high-purity DNA tetrahedral structures with different numbers of extended strands. The concentrations were determined using a micro spectrophotometer. The sequences of the DNA strands with extended strands are shown in SEQ ID NO:33-50.

[0037] 2. In the process of constructing the molecular system, a 20 bp DNA tetrahedron is used as the carbon atom, and the extended strand is used as its valence electron. Different extended strands combine with each other to form chemical bonds.

[0038] Alkane molecular system (including single bonds): CH3CH3: Two DNA tetrahedra with a side length of 20 bp and each having a different extended strand were mixed in a 1:1 molar ratio in TM buffer, placed in centrifuge tubes, sealed with plastic film, and incubated in a 37 ℃ water bath for 2 hours to complete assembly. The structural concentration was set to 350 nM.

[0039] CH3CH2CH3: Mix a DNA tetrahedron with a side length of 20 bp and one extended strand, and another DNA tetrahedron with a side length of 20 bp and two identical extended strands at a molar ratio of 2:1 in TM buffer. Place the mixture in a centrifuge tube, seal the tube opening with plastic film, and incubate at 37 ℃ for 2 hours to complete the assembly. The structural concentration is set to 350 nM.

[0040] CH3CH2CH2CH3: Mix two types of DNA tetrahedra with side length of 20 bp and side length of 20 bp with two different extended strands at a molar ratio of 2:1:1 in TM buffer, place in centrifuge tubes, seal the tube opening with plastic film, and incubate in a constant temperature water bath at 37 ℃ for 2 hours to complete assembly. The structural concentration is set to 350 nM.

[0041] Alkene molecular systems (including double bonds): CH2=CH2: Mix two DNA tetrahedra (with different tetrahedral extension strands and side lengths of 20 bp) at a molar ratio of 1:1 in TM buffer, place them in centrifuge tubes, seal the tube openings with plastic film, and incubate in a constant temperature water bath at 37 ℃ for 2 hours to complete the assembly. The structural concentration is set to 350 nM.

[0042] CH2=CHCH3: Mix DNA tetrahedra with a side length of 20 bp and two identical extended strands, DNA tetrahedra with a side length of 20 bp and one extended strand, and DNA tetrahedra with a side length of 20 bp and three extended strands (two of which are identical) at a molar ratio of 1:1:1 in TM buffer. Place the mixture in a centrifuge tube, seal the tube opening with plastic film, and incubate at 37 ℃ for 2 hours to complete the assembly. The structural concentration is set to 350 nM.

[0043] CH3CH=CHCH3: Two DNA tetrahedra with a side length of 20 bp and three extended strands (the two tetrahedra have different extended strands, and two extended strands are the same in each tetrahedron) and a DNA tetrahedron with a side length of 20 bp and one extended strand are mixed in TM buffer at a molar ratio of 1:1:2. The mixture is placed in a centrifuge tube, the tube opening is sealed with plastic film, and incubated in a constant temperature water bath at 37 ℃ for 2 hours to complete the assembly. The structural concentration is set to 350 nM.

[0044] Alkyne molecular system (including triple bond): CH≡CH: Mix two DNA tetrahedra (with different tetrahedral extension strands and side lengths of 20 bp) with three identical extension strands at a molar ratio of 1:1 in TM buffer, place them in centrifuge tubes, seal the tube openings with plastic film, and incubate in a constant temperature water bath at 37 ℃ for 2 hours to complete the assembly. The structural concentration is set to 350 nM.

[0045] CH≡CCH3: Mix DNA tetrahedra with a side length of 20 bp and three identical extended strands, DNA tetrahedra with a side length of 20 bp and one extended strand, and DNA tetrahedra with a side length of 20 bp and four extended strands (three of which are identical) at a molar ratio of 1:1:1 in TM buffer. Place the mixture in a centrifuge tube, seal the tube opening with plastic film, and incubate at 37 ℃ for 2 hours to complete the assembly. The structural concentration is set to 350 nM.

[0046] CH3C≡CCH3: Two DNA tetrahedra with a side length of 20 bp and four extended strands (the two tetrahedra have different extended strands, and three of the extended strands are the same) and a DNA tetrahedra with a side length of 20 bp and one extended strand are mixed in TM buffer at a molar ratio of 1:1:2. The mixture is placed in a centrifuge tube, the tube is sealed with plastic film, and incubated in a constant temperature water bath at 37 ℃ for 2 hours to complete the assembly. The structural concentration is set to 350 nM.

[0047] Separation and recovery were achieved using polyacrylamide gel electrophoresis (PAGE). Polyacrylamide gels with concentrations of 5% and 6% were selected for separation based on the size of the assembled structures. After electrophoresis, the gels were placed on a blue light gel cutter, and the target bands were cut using a clean knife. The target bands were placed in a gel extraction centrifuge column and frozen at -20 °C for 6 minutes. After freezing, the column was centrifuged at 13000 g for 3 minutes, and the solution at the bottom of the centrifuge column was extracted.

[0048] The synthesis of various hydrocarbon molecular systems using DNA tetrahedrons as artificial atoms was verified through atomic force microscopy experiments, such as... Figure 3 As shown, it can be seen that the three bonding types of single bonds, double bonds and triple bonds were successfully simulated, and the successful synthesis of molecular systems including alkanes, alkenes and alkynes was achieved.

[0049] Example 3 In this embodiment, a hydrocarbon derivative molecular system is constructed using DNA tetrahedra of different sizes as artificial atoms. 1. Functional modification of DNA tetrahedral artificial atoms with side lengths of 13 bp, 26 bp, 30 bp, and 37 bp. Equimolar amounts of DNA strands with extended strands were mixed and TM buffer was added to synthesize DNA tetrahedra with extended strands at a final concentration of 1 μM and a final volume of 100 μL. The sample was then placed in a PCR instrument for annealing. The annealing program was 95 °C for 10 minutes, followed by rapid cooling to 4 °C and incubation for 20 minutes. After annealing and assembly, DNA tetrahedra of different sizes with varying numbers of extended strands were synthesized. The sample was then placed in an ultrafiltration tube with a molecular weight cutoff of 30 kDa for ultrafiltration purification to obtain the product. The concentration was determined using a micro spectrophotometer. The sequences of the DNA strands with extended strands are shown in SEQ ID NO:51-62.

[0050] 2. Constructing hydrocarbon derivative molecular systems: B(CH3)3, CH2NH2, CH3OH, CH3OCH3 and CH3Cl.

[0051] B(CH3)3: Mix DNA tetrahedra with a side length of 20 bp and three extended strands with a side length of 13 bp at a molar ratio of 3:1 in TM buffer, place in centrifuge tubes, seal the tube opening with plastic film, and incubate at 37 ℃ for 2 hours to complete assembly. The structural concentration is set to 450 nM.

[0052] CH2NH2: Mix DNA tetrahedra with a side length of 20 bp and a side length of 26 bp with a side length of 16 bp with a side length of 10 bp at a molar ratio in TM buffer, place in centrifuge tubes, seal the tube openings with plastic film, and incubate in a 37 ℃ water bath for 2 hours to complete assembly. The structural concentration is set to 300 nM.

[0053] CH3OH: Mix DNA tetrahedra with a side length of 20 bp and a side length of 30 bp with a side length of 10 bp with a side length of 10 bp at a molar ratio of 1:1 in TM buffer, place in centrifuge tubes, seal the tube openings with plastic film, and incubate in a 37 ℃ constant temperature water bath for 2 hours to complete assembly. The structural concentration is set to 300 nM.

[0054] CH3OCH3: Mix DNA tetrahedra with a side length of 20 bp and two side lengths of 30 bp with a side length of 10 bp with a molar ratio of 2:1 in TM buffer, place in centrifuge tubes, seal the tube opening with plastic film, and incubate in a 37 ℃ constant temperature water bath for 2 hours to complete assembly. The structural concentration is set to 300 nM.

[0055] CH3Cl: Mix DNA tetrahedra with a side length of 20 bp and a side length of 37 bp with a side length of 17 bp at a predetermined concentration in TM buffer, place in centrifuge tubes, seal the tube openings with plastic film, and incubate in a 37 ℃ constant temperature water bath for 2 hours to complete assembly. The structural concentration is set to 300 nM.

[0056] Separation and recovery were achieved using polyacrylamide gel electrophoresis (PAGE). Depending on the size of the assembled structure, 5% or 6% polyacrylamide gels were selected for separation. The target band was recovered from the gel after electrophoresis and placed in a gel extraction centrifuge column, then frozen at -20 °C for 6 minutes. After removal, it was centrifuged at 13000 g for 3 minutes, and the solution at the bottom of the extraction column was extracted.

[0057] The synthetic efficacy of constructing hydrocarbon derivative molecular systems using DNA tetrahedra of different sizes as artificial atoms was verified through atomic force microscopy experiments, such as... Figure 4 As shown, it can be seen that the hydrocarbon derivatives B(CH3)3, CH2NH2, CH3OH, CH3OCH3 and CH3Cl, which are composed of DNA tetrahedra of two different sizes, were successfully simulated and constructed.

[0058] Example 4 In this embodiment, molecular systems are constructed using DNA tetrahedra of different sizes as artificial atoms to simulate organic chemical reactions.

[0059] Equimolar amounts of DNA strands with extended strands were mixed and TM buffer was added to synthesize DNA tetrahedra with different numbers of extended strands to a final concentration of 1 μM and a final volume of 100 μL. The sample was placed in a PCR instrument for annealing. The annealing program was 95 °C for 10 minutes, followed by rapid cooling to 4 °C and holding for 20 minutes. After annealing and assembly, DNA tetrahedra of different sizes with different numbers of extended strands were synthesized. The sample was placed in an ultrafiltration tube with a molecular weight cutoff of 30 kDa for ultrafiltration purification to obtain the product. The concentration was determined using an ultra-micro spectrophotometer.

[0060] DNA tetrahedra with a side length of 20 bp and one extended strand, DNA tetrahedra with a side length of 20 bp and four extended strands, and DNA tetrahedra with a side length of 37 bp and one extended strand were mixed in TM buffer at a molar ratio of 3:1:1. The mixture was placed in centrifuge tubes, the tubes were sealed with plastic film, and incubated in a 37 °C water bath for 2 hours to complete assembly, constructing a molecular system with a specific conformation as the reactant. The DNA strand sequences with extended strands are shown in SEQ ID NO:63-69.

[0061] The separation and recovery were achieved using polyacrylamide gel electrophoresis (PAGE). The gel after electrophoresis was placed on a blue light gel cutter to recover the target bands, yielding high-purity reactants.

[0062] The chemical reaction dissociation and recombination process is simulated by adding a DNA substitution strand. An equimolar amount of substitution strand is added to the reactants and placed in a 37°C water bath for 2 hours. This process dissociates specific DNA tetrahedra from the reaction structure, forming an intermediate structure. Then, DNA tetrahedral monomers with a designed specific extension chain are added in an equimolar ratio to the intermediate and placed in a 37°C water bath for 2 hours for assembly, ultimately forming the final structure, i.e., the new product. The substitution strand sequences are shown in SEQ ID NO:70-75.

[0063] Each process of dynamic control was detected and verified using atomic force microscopy, such as... Figure 5 As shown, Figure 5In the diagram, (a) represents the chemical formula and corresponding molecular system configuration simulating an organic chemical reaction. Figure 5 (b) in the diagram represents the AFM diagram of the reactants, intermediates, and the final new product. It can be seen that: the product of the first stage only contains the initial reactants; in the second stage, because the substitution strand is added, the DNA tetrahedral monomers will dissociate from the reactants, so the AFM can show that in addition to the intermediates, there are also free DNA tetrahedral monomer structures; the product of the third stage includes the final product and a large number of dissociated representative DNA tetrahedral monomers.

[0064] Example 5 In this embodiment, a molecular system is constructed using DNA tetrahedrons with a side length of 20 bp as artificial atoms to achieve dynamic regulation.

[0065] Equimolar amounts of DNA strands with extended strands were mixed and TM buffer was added to synthesize DNA tetrahedra to a final concentration of 1 μM and a final volume of 100 μL. The sample was then placed in a PCR instrument for annealing. The annealing program was 95 °C for 10 minutes, followed by rapid cooling to 4 °C and incubation for 20 minutes. After annealing and assembly, DNA tetrahedra with varying numbers of extended strands and side lengths were synthesized. The sample was then placed in an ultrafiltration tube with a molecular weight cutoff of 30 kDa for ultrafiltration purification to obtain the product. The concentration was determined using an ultra-micro spectrophotometer. The supplementary sequences with extended strands are shown in SEQ ID NO:76-78.

[0066] Six DNA tetrahedra with different extended strands of predetermined concentration were mixed in a molar ratio of 1:1:1:1:1:1 in TM buffer, placed in centrifuge tubes, sealed with plastic film, and incubated in a 37 °C water bath for 2 hours to complete assembly.

[0067] The synthesis of molecular systems was verified using atomic force microscopy experiments, such as... Figure 6 As shown, it can be seen that the synthesis of the molecular system composed of six tetrahedrons was successful.

[0068] The molecular system achieves dynamic regulation through DNA strand substitution. Three DNA tetrahedral extensions correspond to DNA strand substitution sites. Adding a suitable DNA bridging strand in solution (10:1 molar ratio) connects two DNA tetrahedra with complementary extensions. After mixing, incubation at 37°C for 2 hours yields a dynamic configuration change. Then, adding an excess of substitution strand (10:1 molar ratio) and incubating at 37°C for 2 hours dissociates the bridging strand from the molecular system, restoring its configuration. Adding another bridging strand (10:1 molar ratio) connects two more DNA tetrahedra, and incubating at 37°C for 2 hours again dissociates the corresponding bridging strand from the molecular system, restoring its configuration. The bridging chain sequence is shown in SEQ ID NO:79-80, and the substitution chain sequence is shown in SEQ ID NO:81-82.

[0069] Each process of dynamic control was detected and verified using atomic force microscopy, such as... Figure 7 As shown, it can be seen that: (i) the synthesized molecular system was successfully characterized, and three DNA tetrahedra have a free, distinct extended strand. (ii) by adding a bridging strand, the four left tetrahedra of the molecular system were made into rings. (iii) by adding a substitutional strand complementary to the bridging strand, the bridging strand was dissociated from the molecular system, and the molecular system returned to its original conformation. (iv) by adding another bridging strand, the four middle tetrahedra of the molecular system were made into rings. (v) by adding a substitutional strand complementary to another bridging strand, the other bridging strand was dissociated from the molecular system, and the molecular system returned to its original conformation, thus verifying the dynamic motion of the molecular system.

[0070] The sequences used in embodiments 1-5 of this invention are as follows: Synthesize four tetrahedral DNA strands with a side length of 13 bp. SEQ ID NO:1: (Artificial sequence) ACACTACGTCAGAACAGCTTGCATCACAGGTCACCAGAGTA SEQ ID NO:2: (Artificial sequence) ACGAGCGAGTTGAAGTGATGCAAGCTGAATGCGAGGGTCCT SEQ ID NO:3: (Artificial sequence) TCAACTCGCTCGTAACTACACTGTGCAATACTCTGGTGACC SEQ ID NO:4: (Artificial sequence) TCTGACGTAGTGTATGCACAGTGTAGTAAGGACCCTCGCAT Synthesize four tetrahedral DNA strands with a side length of 20 bp. SEQ ID NO:5: (Artificial sequence) CTCAACTGCCTGGTGATACGAGGATGGGCATGCTCTTCCCGACGGTATTGGACCCTCGCATG SEQ ID NO:6: (Artificial sequence) CGATTACAGCTTGCTACACGATTCAGACTTAGGAATGTTCGACATGCGAGGGGTCCAATACCG SEQ ID NO:7: (Artificial sequence) CTACTATGGCGGGTGATAAAACGTGTAGCAAGCTGTAATCGACGGGAAGAGCATGCCCATCC SEQ ID NO:8: (Artificial sequence) TTTATCACCCGCCATAGTAGACGTATCACCAGGCAGTTGAGACGAACATTCCTAAGTCTGAA Synthesize 8 tetrahedral DNA strands with a side length of 26 bp. SEQ ID NO:9: (Artificial sequence) GCCTGGAGATACATGCACATTACGGCTTTCCCTATTAGAAGG SEQ ID NO:10: (Artificial sequence) TCTCAGGTGCGCGTTTCGGTAAGTAGACGGGACCAGTTCGCC SEQ ID NO:11: (Artificial sequence) CGCGCACCTGAGACCTTCTAATAGGGTTTGCGACAGTCGTTC SEQ ID NO:12: (Artificial sequence) AACTAGAATGCCCTTTGGGCTGTTCCGGGTGTGGCTCGTCGG SEQ ID NO:13: (Artificial sequence) GGCCGAGGACTCCTGCTCCCGCTGCGGTTTGGCGAACTGGTCC SEQ ID NO:14: (Artificial sequence) CGTCTACTTACCGTTTCCGACGAGCCACACCCGGAACAGCCC SEQ ID NO:15: (Artificial sequence) GCCGTAATGTGCATGTATCTCCAGGCTTTCCGCAGCGGAGCA SEQ ID NO:16: (Artificial sequence) GGAGTCCTCGGCCTTTGGGCATTCTAGTTGAACGACTGTCGC Synthesize 8 tetrahedral DNA strands with a side length of 30 bp. SEQ ID NO:17: (Artificial sequence) CGTATCACCTGTCCGTCTGAGGCAGTTGAGTTTGATCTCGAACATTCC SEQ ID NO:18: (Artificial sequence) TAAGTCTGAAGATCCTTTTTTATCACCAGCTGCTGCACGCCATAGTAG SEQ ID NO:19: (Artificial sequence) CATGCGAGGACTCGGTCCAATACCGTACTATTTCGATTACAGATCAAA SEQ ID NO:20: (Artificial sequence) GCTACTTGCTACACGTTTGGATCTTCAGACTTAGGAATGTTCGAGATC SEQ ID NO:21: (Artificial sequence) CGTGTAGCAAGTAGCTTTGATCTGTAATCGTTTCTCTACGGGAAGAGC SEQ ID NO:22: (Artificial sequence) ATGCCCATCCGGCTCTTTCTACTATGGCGTGCAGCAGCTGGTGATAAA SEQ ID NO:23: (Artificial sequence) TAGTACGGTATTGGACCGAGTCCTCGCATGTTTCTCAACTGCCTCAGA SEQ ID NO:24: (Artificial sequence) CGGACAGGTGATACGTTTTGAGCCGGATGGGCATGCTCTTCCCGTAGAG Synthesize 8 tetrahedral DNA strands with a side length of 37 bp. SEQ ID NO:25: (Artificial sequence) CCCTGTACTGGCTAGGAATTCACGTTTTAATCTGGGCTTTGGGTTAAGAAACTCCCCG SEQ ID NO:26: (Artificial sequence) CGCTGGAGGCGCATCACCGTTTGCGTATGTGTTCTGTGCGGCCTGCCGTCCCGTGTGGG SEQ ID NO:27: (Artificial sequence) CGGTGATGCGCCTCCAGCGCGGGGAGTTTCTTAACCCTTTCCGACTTACAAGAGCCGG SEQ ID NO:28: (Artificial sequence) GCGAGACTCAGGTGGTGCCTTTGGCATTCGACCAGGAGATATCGCGTTCAGCTATGCCC SEQ ID NO:29: (Artificial sequence) CCCATGAGAATAATACCGCCGATTTACGTCAGTCCGGTTTCCCACACGGGACGGCAGG SEQ ID NO:30: (Artificial sequence) CCGCACAGAACACATACGCTTTGGGCATAGCTGAACGCGATATCTCCTGGTCGAATGCC SEQ ID NO:31: (Artificial sequence) GCCCAGATTAAAACGTGAATTCCTAGCCAGTACAGGGTTTCCGGACTGACGTAAATCG SEQ ID NO:32: (Artificial sequence) GCGGTATTATTCTCATGGGTTTTGGCACCACCTGAGTCTCGCCCGGCTCTTGTAAGTCGG A DNA tetrahedron with a side length of 20 bp and an extended DNA strand. SEQ ID NO:33: (Artificial sequence) GTGCTTGGTAACATAGGTGCACAGCCTCAACTGCCTGGTGATACGAGGATGGGCATGCTCTTCCCGACGGTATTGGACCCTCGCATG SEQ ID NO:34: (Artificial sequence) GCTGTGCACCTATGTTACCAAGCACCTCAACTGCCTGGTGATACGAGGATGGGCATGCTCTTCCCGACGGTATTGGACCCTCGCATG SEQ ID NO:35: (Artificial sequence) GCTGTGCACCTATGTTACCAAGCACCGATTACAGCTTGCTACACGATTCAGACTTAGGAATGTTCGACATGCGAGGGTCCAATACCG SEQ ID NO:36: (Artificial sequence) GCTGTGCACCTATGTTACCAAGCACCTACTATGGCGGGTGATAAAACGTGTAGCAAGCTGTAATCGACGGGAAGAGCATGCCCATCC SEQ ID NO:37: (Artificial sequence) GCTGTGCACCTATGTTACCAAGCACTTTATCACCCGCCATAGTAGACGTATCACCAGGCAGTTGAGACGAACATTCCTAAGTCTGAA SEQ ID NO:38: (Artificial sequence) GGCGTTAGGCTTCGTTGATGGTAGACGATTACAGCTTGCTACACGATTCAGACTTAGGAATGTTCGACATGCGAGGGTCCAATACCG SEQ ID NO:39: (Artificial sequence) TCTACCATCAACGAAGCCTAACGCCCTACTATGGCGGGTGATAAAACGTGTAGCAAGCTGTAATCGACGGGAAGAGCATGCCCATCC SEQ ID NO:40: AAAGCCGGTAAGGTGAGGAATCCGACTACTATGGCGGGTGATAAAACGTGTAGCAAGCTGTAATCGACGGGAAGAGCATGCCCATCC SEQ ID NO:41: TCGGATTCCTCACCTTACCGGCTTTCGATTACAGCTTGCTACACGATTCAGACTTAGGAATGTTCGACATGCGAGGGTCCAATACCG SEQ ID NO:42: TCGGATTCCTCACCTTACCGGCTTTTTTATCACCCGCCATAGTAGACGTATCACCAGGCAGTTGAGACGAACATTCCTAAGTCTGAA SEQ ID NO:43: ACCTGAGTGAGTATGCGGAGTACGATTTATCACCCGCCATAGTAGACGTATCACCAGGCAGTTGAGACGAACATTCCTAAGTCTGAA SEQ ID NO:44: TCGTACTCCGCATACTCACTCAGGTTTTATCACCCGCCATAGTAGACGTATCACCAGGCAGTTGAGACGAACATTCCTAAGTCTGAA SEQ ID NO:45: AAAAAAAAAAAAAAAAAAAAAAACTCAACTGCCTGGTGATACGAGGATGGGCATGCTCTTCCCGACGGTATTGGACCCTCGCATG SEQ ID NO:46: AAAAAAAAAAAAAAAAAAAAAAAAACTACTATGGCGGGTGATAAAACGTGTAGCAAGCTGTAATCGACGGGAAGAGCATGCCCATCC SEQ ID NO:47: (Artificial sequence) AAAAAAAAAAAAAAAAAAAAAAAAATTTATCACCCGCCATAGTAGACGTATCACCAGGCAGTTGAGACGAACATTCCTAAGTCTGAA SEQ ID NO:48: (Artificial sequence) TTTTTTTTTTTTTTTTTTTTTTTCTCAACTGCCTGGTGATACGAGGATGGGCATGCTCTTCCCGACGGTATTGGACCCTCGCATG SEQ ID NO:49: (Artificial sequence) TTTTTTTTTTTTTTTTTTTTTTCTACTATGGCGGGTGATAAAACGTGTAGCAAGCTGTAATCGACGGGAAGAGCATGCCCATCC SEQ ID NO:50: (Artificial sequence) TTTTTTTTTTTTTTTTTTTTTTTTTTATCACCCGCCATAGTAGACGTATCACCAGGCAGTTGAGACGAACATTCCTAAGTCTGAA A 13 bp tetrahedral DNA strand with an extended strand. SEQ ID NO:51: (Artificial sequence) GTGCTTGGTAACATAGGTGCACAGCACACTACGTCAGAACAGCTTGCATCACAGGTCACCAGAGTA SEQ ID NO:52: (Artificial sequence) GTGCTTGGTAACATAGGTGCACAGCACGAGCGAGTTGAAGTGATGCAAGCTGAATGCGAGGGTCCT SEQ ID NO:53: (Artificial sequence) GTGCTTGGTAACATAGGTGCACAGCTCAACTCGCTCGTAACTACACTGTGCAATACTCTGGTGACC A DNA tetrahedron with an extension strand and a side length of 26 bp. SEQ ID NO:54: (Artificial sequence) AAAGCCGGTAAGGTGAGGAATCCGAGGCCGAGGACTCCTGCTCCCGCTGCGGTTTGGC GAACTGGTCC SEQ ID NO:55: (Artificial sequence) ACCTGAGTGAGTATGCGGAGTACGAGCCTGGAGATACATGCACATTACGGCTTTCCCTATTAGAAGG SEQ ID NO:56: (Artificial sequence) GGCGTTAGGCTTCGTTGATGGTAGACGCGCACCTGAGACCTTCTAATAGGGTTTGCGACAGTCGTTC SEQ ID NO:57: (Artificial sequence) ACCTGAGTGAGTATGCGGAGTACGAGCCGTAATGTGCATGTATCTCCAGGCTTTCCGCAGCGGAGCA A 30 bp tetrahedral DNA strand with an extended strand. SEQ ID NO:58: (Artificial sequence) TCTACCATCAACGAAGCCTAACGCCCGTGTAGCAAGTAGCTTTGATCTGTAATCGTTTCTCTACGGGAAGAGC SEQ ID NO:59: (Artificial sequence) TCGGATTCCTCACCTTACCGGCTTTTAGTACGTATTGGACCGAGTCCTCGCATGTTTCTCAACTGCCTCAGA A DNA tetrahedron with an extended strand and a side length of 37 bp. SEQ ID NO:60: (Artificial sequence) GCTGTGCACCTATGTTACCAAGCACCCCTGTACTGGCTAGGAATTCACGTTTTAATCTGGGCTTTGGGTTAAGAAACTCCCCG SEQ ID NO:61: (Artificial sequence) TCGGATTCCTCACCTTACCGGCTTTCGGTGATGCGCCTCCAGCGCGGGGAGTTTCTTAACCCTTTCCGACTTACAAGAGCCGG SEQ ID NO:62: (Artificial sequence) TTTTTTTTTTTTTTTTTTTTTTTGCCCAGATTAAAACGTGAATTCCTAGCCAGTACAGGGTTTCCGGACTGACGTAAATCG DNA strands with sides of 20 bp, tetrahedral with extended strands, used to simulate organic reactions. SEQ ID NO:63: (Artificial sequence) CTCCGCATACTCACTCAGGTCGATTACAGCTTGCTACACGATTCAGACTTAGGAATGTTCGACATGCGAGGGTCCAATACCG SEQ ID NO:64: (Artificial sequence) CTCAACTGCCTGGTGATACGAGGATGGGCATGCTCTTCCCGACGGTATTGGACCCTCGCATGCTCCGCATAC SEQ ID NO:65: (Artificial sequence) TCACTCAGGTCTCAACTGCCTGGTGATACGAGGATGGGCATGCTCTTCCCGACGGTATTGGACCCTCGCATG SEQ ID NO:66: (Artificial sequence) CTCAACTGCCTGGTGATACGAGGATGGGCATGCTCTTCCCGACGGTATTGGACCCTCGCATGGTATGCGGAG SEQ ID NO:67: (Artificial sequence) ACCTGAGTGACTCAACTGCCTGGTGATACGAGGATGGGCATGCTCTTCCCGACGGTATTGGACCCTCGCATG DNA strands with sides of 30 bp, tetrahedral with extended strands, used to simulate organic reactions. SEQ ID NO:68: (Artificial sequence) ACCTGAGTGAGTATGCGGAGCGTATCACCTGTCCGTCTGAGGCAGTTGAGTTTGATCT CGAACATTCC DNA strands with sides of 37 bp, tetrahedral with extended strands, used to simulate organic reactions. SEQ ID NO:69: (Artificial sequence) TACGAACCTGAGTGAGTATGCGGAGCCCTGTACTGGCTAGGAATTCACGTTTTAATCTGGGCTTTGGGTTAAGAAACTCCCCG SEQ ID NO:70: (Artificial sequence) CTCCGCATACTCACTCAGGTTCGTA SEQ ID NO:71: (Artificial sequence) ATGCTACCTGAGTGAGTGCTGTATGCGGAG SEQ ID NO:72: (Artificial sequence) CTCCGCATACAGCACTCACTCAGGTAGCAT SEQ ID NO:73: (Artificial sequence) ATCCATCACTCAGGTGAGATCTCCGCATAC SEQ ID NO:74: (Artificial sequence) GTATGCGGAGATCTCACCTGAGTGATGGAT SEQ ID NO:75: (Artificial sequence) AGCTCGTTCGTTGATGGTAGACGCAGTGAGTATGCGGAG A 20 bp tetrahedral DNA strand with an extended strand. SEQ ID NO:76: (Artificial sequence) CTCAACTGCCTGGTGATACGAGGATGGGCATGCTCTTCCCGACGGTATTGGACCCTCGCATGGACGATTCCGCAGTA SEQ ID NO:77: (Artificial sequence) CTGCAAGCCTCAGCACTCAACTGCCTGGTGATACGAGGATGGGCATGCTCTTCCCGACGGTATTGGACCCTCGCATG SEQ ID NO:78: (Artificial sequence) ATCCCGGTTCTTGTCACGATTACAGCTTGCTACACGATTCAGACTTAGGAATGTTCGACATGCGAGGGTCCAATACCG Bridge chain SEQ ID NO:79: (Artificial sequence) TGCTGAGGCTTGCAGTTTTTACTGCGGAATCGTCTCCGTGGTGT SEQ ID NO:80: (Artificial sequence) ACACCACGGAGACGATTCCGCAGTAAAAACTGCAAGCCTCAGCA Replacement chain SEQ ID NO:81: (Artificial sequence) TGACAAGAACCGGATTTTTACAGACCAGGCGCATTATGTTGCCA SEQ ID NO:82: (Artificial sequence) TGGCAACATAATGCGCCTGGTCTGTAAAAATCCGGTTCTTGTCA In the description of this specification, references to terms such as "an embodiment," "example," "specific example," etc., indicate that a specific feature, structure, material, or characteristic described in connection with that embodiment or example is included in at least one embodiment or example of the invention. In this specification, 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.

[0071] 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 to the above embodiments. The embodiments and descriptions in the specification are merely illustrative of the principles of the invention. Various changes and modifications can be made to the invention without departing from its spirit and scope, and all such changes and modifications fall within the scope of the claimed invention.

Claims

1. A method for constructing a molecular system based on DNA nanostructured artificial atoms, characterized in that, Includes the following steps: DNA strands with extended strands are mixed, added to TM buffer solution, and then annealed to synthesize DNA nanostructures with extended strands. Artificial atoms are represented by DNA nanostructures, valence electrons are represented by the extended strands on the DNA nanostructures, and chemical bonds are represented by the double strands formed by the interaction between the extended strands. According to the target molecular configuration, multiple DNA nanostructures with extended strands are mixed in proportion and assembled into a molecular system through a one-pot method.

2. The method for constructing a molecular system based on DNA nanostructured artificial atoms according to claim 1, characterized in that, The DNA nanostructure is a DNA tetrahedron, a DNA cube, a DNA octahedron, or any three-dimensional nanostructure constructed using DNA origami technology.

3. The method for constructing a molecular system based on DNA nanostructured artificial atoms according to claim 1, characterized in that, The annealing process is as follows: hold at 95°C for 10 minutes, then cool down to 4°C and hold for 20 minutes.

4. The method for constructing a molecular system based on DNA nanostructured artificial atoms according to claim 1, characterized in that, The DNA strand with an extended strand includes DNA strands as shown in SEQ ID NO:33~78.

5. The method for constructing a molecular system based on DNA nanostructured artificial atoms according to claim 1, characterized in that, The molecular system includes one or more of the following: linear structure, cyclic structure, branched structure, two-dimensional network structure, or three-dimensional spatial structure.

6. A programmable molecular system, characterized in that, It is constructed using the construction method described in any one of claims 1-5.

7. The application of the programmable molecular system according to claim 6 in simulating chemical reactions.

8. The method for simulating chemical reactions using the programmable molecular system as described in claim 6, characterized in that, Includes the following steps: After mixing the programmable molecular system with the substitution chain, the reaction is carried out by heating in a water bath, and the reaction is dissociated to form an intermediate. DNA nanostructures with extended strands are mixed with intermediates and self-assembled by heating in a water bath to form new molecular systems.

9. The dynamic control method for a programmable molecular system according to claim 6, characterized in that, Includes the following steps: In a solution environment, the molecular system is mixed with the bridging chain and reacted by heating in a water bath, so that the bridging chain and the extended chain in the molecular system are partially complementary, thereby achieving the combination of double chains. An excess of substitutional chain is added to the molecular system after the bridging chain is combined, and the reaction is carried out by heating in a water bath. The substitutional chain combines with the double chain and replaces the original bridging chain, thus restoring the configuration of the molecular system.

10. The method for dynamic control of a programmable molecular system according to claim 9, characterized in that, The bridging chain sequence is shown in SEQ ID NO:79-80, and the substitution chain sequence is shown in SEQ ID NO:81-82.

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