Microelectrode array and simulation method for synthesizing DNA by using microelectrode array

Abstract

The microelectrode array comprises a plurality of microelectrode cells, the microelectrode cell comprises a working electrode and a counter electrode, and the counter electrode generates alkaline ions to neutralize hydrogen ions generated by the working electrode. A simulation method for synthesizing DNA by using a microelectrode array comprises the following steps: establishing a three-dimensional model of the microelectrode array by using multi-physical field simulation software, and solving and calculating a physical field to obtain a calculation result; and post-processing the calculation result, and creating a drawing group about the hydrogen ion concentration. According to the microelectrode array and the simulation method of the synthesized DNA of the microelectrode array, the counter electrode is added into the microelectrode array, hydrogen ions generated by the working electrode are neutralized through basic ions generated by the counter electrode, crosstalk of the hydrogen ions is avoided, modeling analysis is conducted on the crosstalk condition of the hydrogen ions generated by the working electrode through multi-physics field simulation software, and the simulation result of the synthesized DNA of the microelectrode array is obtained. And theoretical guidance is provided for high-throughput synthesis of different types of DNA.

Description

Technical Field

[0001] This invention belongs to the field of electrochemical DNA synthesis, and particularly relates to a microelectrode array and a simulation method for DNA synthesis. Background Technology

[0002] With the development of information technology, the scale of data has exploded, and existing storage media are gradually approaching their density limits, prompting the search for new storage media. DNA (Deoxyribonucleic acid) has advantages such as high storage density, long storage time, and simple maintenance, and is considered one of the most promising emerging storage media. However, the low throughput and high cost of DNA synthesis limit the widespread application of DNA data storage.

[0003] Currently, DNA synthesis methods are mainly divided into chemical and biological methods. Traditional phosphorus amide chemical synthesis, represented by first-generation solid-phase column synthesis, is efficient but has low throughput and high cost. Third-generation enzyme-based biological methods are environmentally friendly and efficient, but are currently still in the technology verification stage. Second-generation electrochemical methods based on phosphorus amide utilize microelectrode arrays. Under energized conditions, proton acids are generated in situ on the anode surface of the electrodes to remove DMT protecting groups, achieving DNA synthesis on the electrode surface. This method also features extremely high microelectrode array density, enabling parallel high-throughput DNA synthesis, and is an effective solution to the aforementioned problems.

[0004] However, the second-generation electrochemical method based on phosphoramide has a high electrode density in the microelectrode array and the electrodes are very close together (about a few micrometers). The deprotected hydrogen ions generated on the electrode surface may diffuse to adjacent electrodes, causing unnecessary deprotection and resulting in hydrogen ion crosstalk. Summary of the Invention

[0005] This application provides a microelectrode array and a simulation method for synthesizing DNA. A counter electrode is added to the microelectrode array, and the alkaline ions generated by the counter electrode neutralize the hydrogen ions generated by the working electrode, thus avoiding hydrogen ion crosstalk. Multiphysics simulation software is used to model and analyze the hydrogen ion crosstalk generated by the working electrode, providing theoretical guidance for high-throughput synthesis of different types of DNA.

[0006] Other objects and advantages of the present invention can be further understood from the technical features disclosed herein.

[0007] To achieve one or more of the above objectives or other objectives, the present invention provides a microelectrode array and a method for simulating DNA synthesis therefrom.

[0008] A microelectrode array, comprising:

[0009] Several microelectrode cells;

[0010] The microelectrode cell includes a working electrode and a counter electrode, wherein the counter electrode generates alkaline ions to neutralize the hydrogen ions generated by the working electrode.

[0011] The microelectrode cell consists of one working electrode and four counter electrodes, and the area ratio of the working electrode to the counter electrodes is less than or equal to 2 / 5.

[0012] The microelectrode cell has counter electrodes of the same shape and size symmetrically distributed at its four corners, and a working electrode is located at its center.

[0013] The working electrode consists of an upper cylinder and a lower cylinder, wherein the radius of the upper cylinder is greater than the radius of the lower cylinder, and the height of the upper cylinder is greater than the height of the lower cylinder.

[0014] The counter electrode has a regular triangular prism structure; the three lateral edges of the regular triangular prism intersect the border line of the microelectrode cell and are perpendicular to the border line of the microelectrode cell.

[0015] The upper surface of the cylinder on the working electrode and the upper surface of the counter electrode are located on the same horizontal plane.

[0016] In an N×N microelectrode array composed of several microelectrode cells, the counter electrodes of adjacent cells can be combined.

[0017] The counter electrodes of four adjacent cells can be combined to form a cube counter electrode, and the distance between the working electrodes in the microelectrode array is equal to the distance between the cube counter electrodes.

[0018] A simulation method for synthesizing DNA using a microelectrode array, comprising:

[0019] Determine the relevant parameters in multiphysics simulation software;

[0020] Multiphysics simulation software builds a three-dimensional model of the microelectrode array based on relevant parameters;

[0021] Choose a suitable physics interface and determine the initial values ​​and boundary conditions;

[0022] The microelectrode array is meshed;

[0023] Add transient studies, set the output time step, solve the physical field and output the calculation results;

[0024] The calculation results are post-processed to create a plotting group of hydrogen ion concentrations.

[0025] The specific process of selecting a suitable physics interface and determining initial values ​​and boundary conditions includes:

[0026] Construct control equations for multiphysics processes of reaction engineering, chemistry, and rare mass transport in multiphysics simulation software;

[0027] Select a suitable physics interface: The physics interface is selected as rare matter transfer, and the research type is selected as transient.

[0028] Set initial values: The initial values ​​are set as the initial concentrations of each substance in the reaction process;

[0029] Set boundary conditions: The boundary conditions are open boundary and electrode surface coupling.

[0030] The plotting group includes isosurface plots and contour plots of hydrogen ion concentration.

[0031] Compared with the prior art, the beneficial effects of the present invention mainly include:

[0032] This application provides a microelectrode array and a simulation method for synthesizing DNA. A counter electrode is added to the microelectrode array, and the alkaline ions generated by the counter electrode neutralize the hydrogen ions generated by the working electrode, thus avoiding hydrogen ion crosstalk. Multiphysics simulation software is used to model and analyze the hydrogen ion crosstalk generated by the working electrode, providing theoretical guidance for high-throughput synthesis of different types of DNA.

[0033] To make the above and other objects, features and advantages of the present invention more apparent and understandable, preferred embodiments are described below in detail with reference to the accompanying drawings. Attached Figure Description

[0034] To more clearly illustrate the technical solutions in the specific embodiments of the present invention, the drawings used in the description of the embodiments will be briefly introduced below. Obviously, the drawings described below are only some embodiments of the present invention. For those skilled in the art, other drawings can be obtained based on these drawings without creative effort.

[0035] Figure 1 This is a schematic diagram of a microelectrode array structure provided in Embodiment 1 of this application.

[0036] Figure 2 This is a schematic diagram of a simulation method for synthesizing DNA using a microelectrode array, provided in Embodiment 2 of this application.

[0037] Figure 3 This is a three-dimensional structural model diagram of the microelectrode array provided in Embodiment 2 of this application.

[0038] Figure 4 This is a mesh partitioning diagram of the three-dimensional model of the microelectrode array provided in Embodiment 2 of this application.

[0039] Figure 5 The isosurface plot of the hydrogen ion concentration of the working electrode provided in Embodiment 2 of this application.

[0040] Figure 6 The contour plot of hydrogen ion concentration of the working electrode based on the first cross section is provided for Embodiment 2 of this application.

[0041] Figure 7 The working electrode hydrogen ion concentration based on the second cross section is provided for Embodiment 2 of this application. Figure 1 .

[0042] Figure 8 The working electrode hydrogen ion concentration based on the second cross section is provided for Embodiment 2 of this application. Figure 2 .

[0043] Figure 9 The working electrode hydrogen ion concentration based on the second cross section is provided for Embodiment 2 of this application. Figure 3 . Detailed Implementation

[0044] The foregoing and other technical contents, features, and effects of the present invention will be clearly presented in the following detailed description of a preferred embodiment with reference to the accompanying drawings. The directional terms mentioned in the following embodiments, such as up, down, left, right, front, or back, are merely for reference to the accompanying drawings. Therefore, the directional terms used are for illustrative purposes and not for limiting the present invention.

[0045] This application provides a microelectrode array and a simulation method for synthesizing DNA. A counter electrode is added to the microelectrode array, and the alkaline ions generated by the counter electrode neutralize the hydrogen ions generated by the working electrode, thus avoiding hydrogen ion crosstalk. Multiphysics simulation software is used to model and analyze the hydrogen ion crosstalk generated by the working electrode, providing theoretical guidance for high-throughput synthesis of different types of DNA.

[0046] The embodiments of this application will now be described in detail with reference to the accompanying drawings. However, those skilled in the art will understand that many technical details have been provided in the embodiments of this application to facilitate a better understanding of the application. However, the technical solutions claimed in this application can be implemented even without these technical details and various variations and modifications based on the following embodiments.

[0047] Example 1

[0048] Figure 1 The diagram shown is a schematic diagram of a microelectrode array structure provided in Embodiment 1 of this application.

[0049] like Figure 1 As shown, a microelectrode array includes: a plurality of microelectrode cells 1.

[0050] Microelectrode cell 1 consists of one working electrode and four counter electrodes. The alkaline ions generated by the counter electrodes can neutralize the hydrogen ions generated by the working electrode.

[0051] like Figure 1 As shown, counter electrodes of the same shape and size are symmetrically distributed at the four corners of microelectrode cell 1, and a working electrode is set at the center. The working electrode consists of an upper cylinder and a lower cylinder, with the radius of the upper cylinder being greater than that of the lower cylinder and the height of the upper cylinder being greater than that of the lower cylinder. The counter electrode is a regular triangular prism structure, and the three lateral edges of the regular triangular prism intersect with the border line of microelectrode cell 1 and are perpendicular to the border line of microelectrode cell 1.

[0052] In microelectrode cell 1, the area ratio of the working electrode to the counter electrode is less than or equal to 2 / 5, and the upper surface of the cylinder on the working electrode and the upper surface of the counter electrode are located on the same horizontal plane.

[0053] like Figure 1 As shown, in an N×N microelectrode array composed of several microelectrode cells 1, the counter electrodes of adjacent cells can be combined; the counter electrodes of four adjacent cells can be combined into a cube counter electrode, and the distance between the working electrodes in the microelectrode array is equal to the distance between the cube counter electrodes.

[0054] Figure 2 This is a schematic diagram of a simulation method for synthesizing DNA using a microelectrode array, provided in Embodiment 2 of this application.

[0055] like Figure 2 As shown, a simulation method for synthesizing DNA using a microelectrode array is described. This method utilizes multiphysics simulation software to establish a three-dimensional model of the microelectrode array, including:

[0056] Determine the relevant parameters in multiphysics simulation software;

[0057] Multiphysics simulation software builds a three-dimensional model of the microelectrode array based on relevant parameters;

[0058] Choose a suitable physics interface and determine the initial values ​​and boundary conditions;

[0059] Mesh the microelectrode array;

[0060] Add transient studies, set the output time step, solve the physical field and output the calculation results;

[0061] The calculation results were post-processed to create a plotting group including hydrogen ion concentration isosurface map and hydrogen ion concentration contour map to study the hydrogen ion crosstalk generated by the working electrode in the microelectrode array.

[0062] The specific process of selecting a suitable physical field interface and determining initial values ​​and boundary conditions includes:

[0063] Construct control equations for multiphysics processes of reaction engineering, chemistry, and rare mass transport in multiphysics simulation software;

[0064] Choose the appropriate physics interface: Select rare matter transfer for the physics interface, and select transient for the research type;

[0065] Set initial values: The initial values ​​are set to the initial concentrations of each substance in the reaction process;

[0066] Set boundary conditions: The boundary conditions are open boundary and electrode surface coupling.

[0067] Specifically, taking a 3×3 microelectrode array as an example, the steps include:

[0068] Step S1: Determine the relevant parameters during the simulation process;

[0069] Table 1 is a simulation parameter table provided in Embodiment 2 of this application. The relevant parameters in the simulation process are shown in Table 1:

[0070]

[0071]

[0072] Table 1

[0073] Step S2: Establish a three-dimensional model of the 3×3 microelectrode array based on relevant parameters;

[0074] Figure 3 This is a three-dimensional structural model diagram of the microelectrode array provided in Embodiment 2 of this application.

[0075] like Figure 3 As shown, the influence range (study area) of hydrogen ion concentration in this application is an upper hemisphere with a radius of 100 micrometers.

[0076] like Figure 1 As shown, the working electrode consists of an upper cylinder with a radius of 0.75 μm and a height of 0.36 μm and a lower cylinder with a radius of 0.5 μm and a height of 0.1 μm. The counter electrode is a regular triangular prism, with all three lateral edges intersecting and perpendicular to the border lines of microelectrode cell 1. In an N×N microelectrode array composed of several microelectrode cells 1, the counter electrodes of adjacent cells can be combined; four adjacent cells can be combined to form a cube counter electrode with a side length of 1 μm and a height of 0.2 μm.

[0077] In microelectrode cell 1, the area ratio of the working electrode to the counter electrode is less than or equal to 2 / 5, and the upper surface of the cylinder on the working electrode and the upper surface of the counter electrode are located on the same horizontal plane; the distance between the working electrodes in the microelectrode array is equal to the distance between the cube counter electrodes, the distance between the working electrodes is 3 micrometers, and the distance between the cube counter electrodes is 3 micrometers.

[0078] Step S3: Select a suitable physics interface and determine the initial values ​​and boundary conditions:

[0079] Specifically, control equations for multiphysics processes of reaction engineering, chemistry, and rare matter transport are constructed in multiphysics simulation software;

[0080] In "Reaction Engineering", add the following reaction:

[0081] Reaction 1:

[0082] Reaction 2: CH3OH + 2e - →CH3O - +H2

[0083] Reaction 3: CH3O - +H + →CH3OH

[0084] Correspondingly, the operation of the microelectrode array is as follows:

[0085] Reaction 1 produces hydrogen ions, which then react in the working electrode;

[0086] Reaction 2 produces basic ions, which react in the counter electrode;

[0087] Reaction 3 is a neutralization reaction between basic ions and hydrogen ions.

[0088] Initial values ​​are set as follows: the initial concentration of C6H4(OH)2 is Cred, the initial concentration of C6H4O2 is Cben, and the initial concentration of CH3OH is Cmethanol.

[0089] Select the appropriate physics interface: Select "Rare Matter Transfer (tds)" for the physics interface and "Transient" for the research type;

[0090] The rare substance transport process is represented as:

[0091]

[0092] In the above formula, To differentiate the formula, C i Let t be the concentration of the substance and t be the time. For Hamiltonian operators, J i For the diffusion term, R iFor the reaction source term, D i denoted as the diffusion coefficient of the substance.

[0093] Set boundary conditions: The boundary conditions for "Dilute Material Transfer (tds)" are "Open Boundary" and "Electrode Surface Coupling".

[0094] The local current density on the electrode surface can be calculated using the Butler-Volmer equation:

[0095]

[0096] In the above formula, i loc Let n be the local current density, n be the electron transfer number, F be the Faraday constant, K be the heterogeneous reaction rate of the oxidation reaction, α be the charge transfer number, R be the gas constant, T be the temperature, and η be the overpotential. red C represents the concentration of the reducing agent. ox This represents the oxide concentration.

[0097] Specifically, in an open boundary, the external concentration

[0098] In surface coupling of the working electrode:

[0099]

[0100] Where the number of participating electrons is n = n1, and the stoichiometric coefficient is V cC6H4OH2 =1,V cC6H4O2 =-1,V cCH_1p =-2.

[0101] In electrode surface coupling:

[0102]

[0103] Where the number of participating electrons is n = n1, and the stoichiometric coefficient is V cCH3O_1m =2,V cCH3OH =-2,V cCH2_gas =1.

[0104] In the above formula, step1(t[1 / s]) is the step function set in the multiphysics simulation software (COMSOL), and its specific parameters are: position 250, from 0 to 1, transition region size 750, and continuous derivative order 1.

[0105] Figure 4 This is a mesh partitioning diagram of the three-dimensional model of the microelectrode array provided in Embodiment 2 of this application.

[0106] Step S4: Select a suitable meshing method to mesh the microelectrode array and obtain a 3×3 microelectrode array meshing diagram.

[0107] Specifically, the sequence type is selected as "User-Controlled Network," and the mesh size is selected as "Ultra-fine." A free tetrahedral mesh is constructed for the 3×3 microelectrode array, with the mesh size selected as "Extremely Fine." The resulting mesh generation diagram of the 3×3 microelectrode array is shown below. Figure 4 As shown.

[0108] Step S5: Add transient study, set output time step, solve and calculate the physical field of reaction engineering, chemistry, and rare matter transfer, and output the calculation results;

[0109] The output timing is: start time 0s, step size 1s, stop time 60s.

[0110] Step S6: Post-process the calculation results and create a plotting group including hydrogen ion concentration isosurface map and hydrogen ion concentration contour map to study the hydrogen ion crosstalk generated by the working electrode in the microelectrode array.

[0111] Figure 5 The image shown is a contour plot of the hydrogen ion concentration of the working electrode of the 3×3 microelectrode array provided in Embodiment 2 of this application.

[0112] like Figure 5 As shown, the concentration of hydrogen ions generated by the working electrode in the microelectrode array is 1×10^(-3) mol / L.

[0113] Figure 6 The figure shown is a contour plot of the hydrogen ion concentration of the working electrode of the 3×3 microelectrode array provided in Embodiment 2 of this application, based on the first cross section.

[0114] like Figure 6 As shown, the first cross-section is Figure 5 The concentration of hydrogen ions generated by the working electrode in the microelectrode array along the X-axis is 1×10^(-3) mol / L.

[0115] Figure 7 The figure shown is a contour line of hydrogen ion concentration based on the second cross section of the working electrode of the 3×3 microelectrode array provided in Embodiment 2 of this application. Figure 1 .

[0116] Figure 8 The figure shown is a contour line of hydrogen ion concentration based on the second cross section of the working electrode of the 3×3 microelectrode array provided in Embodiment 2 of this application. Figure 2 .

[0117] Figure 9 The figure shown is a contour line of hydrogen ion concentration based on the second cross section of the working electrode of the 3×3 microelectrode array provided in Embodiment 2 of this application. Figure 3 .

[0118] Specifically, the second cross section is Figure 5 The cross section along the Z-axis.

[0119] like Figure 7-9 As shown, with the increase of time, the concentration of hydrogen ions generated by the working electrode in the microelectrode array first gradually increases, and then gradually decreases because the alkaline ions generated by the counter electrode neutralize some of the hydrogen ions generated by the working electrode.

[0120] This application provides a microelectrode array and a simulation method for synthesizing DNA. A counter electrode is added to the microelectrode array, and the alkaline ions generated by the counter electrode neutralize the hydrogen ions generated by the working electrode, thus avoiding hydrogen ion crosstalk. Multiphysics simulation software is used to model and analyze the hydrogen ion crosstalk generated by the working electrode, providing theoretical guidance for high-throughput synthesis of different types of DNA.

[0121] The common English terms or letters used in this invention for clarity of description are for illustrative purposes only and are not limiting interpretations or specific uses. They should not be used to limit the scope of protection of this invention based on their possible Chinese translations or specific letters.

[0122] It should also be noted that in this article, relational terms such as “first” and “second” are used only to distinguish one entity or operation from another, and do not necessarily require or imply any such actual relationship or order between these entities or operations.

Claims

1. A microelectrode array, characterized in that, include: Several microelectrode cells; The microelectrode cell includes a working electrode and a counter electrode, wherein the counter electrode generates alkaline ions to neutralize the hydrogen ions generated by the working electrode.

2. The microelectrode array according to claim 1, characterized in that, The microelectrode cell consists of one working electrode and four counter electrodes, and the area ratio of the working electrode to the counter electrodes is less than or equal to 2 / 5.

3. A microelectrode array according to claim 2, characterized in that, The microelectrode cell has counter electrodes of the same shape and size symmetrically distributed at its four corners, and a working electrode is located at its center.

4. A microelectrode array according to claim 3, characterized in that, The working electrode consists of an upper cylinder and a lower cylinder, wherein the radius of the upper cylinder is greater than the radius of the lower cylinder, and the height of the upper cylinder is greater than the height of the lower cylinder.

5. A microelectrode array according to claim 4, characterized in that, The counter electrode has a regular triangular prism structure; the three lateral edges of the regular triangular prism intersect the border line of the microelectrode cell and are perpendicular to the border line of the microelectrode cell.

6. A microelectrode array according to claim 5, characterized in that, The upper surface of the cylinder on the working electrode and the upper surface of the counter electrode are located on the same horizontal plane.

7. A microelectrode array according to claim 5, characterized in that, In an N×N microelectrode array composed of several microelectrode cells, the counter electrodes of adjacent cells can be combined. The counter electrodes of four adjacent cells can be combined to form a cube counter electrode, and the distance between the working electrodes in the microelectrode array is equal to the distance between the cube counter electrodes.

8. A simulation method for synthesizing DNA using a microelectrode array, characterized in that, Using a microelectrode array according to any one of claims 1-7, comprising: Determine the relevant parameters in multiphysics simulation software; Multiphysics simulation software builds a three-dimensional model of the microelectrode array based on relevant parameters; Choose a suitable physics interface and determine the initial values ​​and boundary conditions; The microelectrode array is meshed; Add transient studies, set the output time step, solve the physical field and output the calculation results; The calculation results are post-processed to create a plotting group of hydrogen ion concentrations.

9. The simulation method for DNA synthesis using a microelectrode array according to claim 8, characterized in that, The specific process of selecting a suitable physics interface and determining initial values ​​and boundary conditions includes: Construct control equations for multiphysics processes of reaction engineering, chemistry, and rare mass transport in multiphysics simulation software; Select a suitable physics interface: The physics interface is selected as rare matter transfer, and the research type is selected as transient. Set initial values: The initial values ​​are set as the initial concentrations of each substance in the reaction process; Set boundary conditions: The boundary conditions are open boundary and electrode surface coupling.

10. The simulation method for DNA synthesis using a microelectrode array according to claim 8, characterized in that, The plotting group includes isosurface plots and contour plots of hydrogen ion concentration.

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