CN112562800A - Map dyeing and recombination method of addressable DNA polyhedron topological structure - Google Patents
Map dyeing and recombination method of addressable DNA polyhedron topological structure Download PDFInfo
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Abstract
The invention relates to the technical field of DNA polyhedron dyeing and recombination, in particular to a graph dyeing and recombination method of an addressable DNA polyhedron topological structure, which can solve the problem of conflict between repeatability and addressability in the DNA polyhedron topological structure consisting of repeated components. A method for map staining of addressable DNA polyhedron topology comprising: step 1, dyeing each edge of a DNA polyhedron by using two colors, wherein the number of the edges of the two colors is equal, the edge of each color corresponds to an addressable component, and the addressable component comprises a first addressable component and a second addressable component; step 2, synthesizing a DNA dyed chain by utilizing a plurality of first addressable components and/or a plurality of second addressable components, wherein the DNA dyed chain corresponds to a number; a plurality of DNA staining chains correspond to a plurality of numbers one by one; and 3, optimizing the plurality of DNA dyed chains to obtain the standard DNA dyed chains. The invention is used for map staining and recombination of addressable DNA polyhedron topological structure.
Description
Technical Field
The invention relates to the technical field of DNA polyhedron dyeing and recombination, in particular to a map dyeing and recombination method of an addressable DNA polyhedron topological structure.
Background
The DNA nanotechnology is a method for designing and constructing a complex structure and accurately controlling the nanometer characteristics of the complex structure by taking DNA as a synthetic material. The purpose is to synthesize a three-dimensional or two-dimensional nanostructure using a DNA strand as a raw material. DNA is suitable for creating nanoscale structures because the binding between nucleic acid strands follows the well-known rules of simple base pairing, forming unique double-helical nanostructures. By utilizing this property, the assembly of the structure can be easily controlled by the design of the nucleic acid strand.
Due to the special base complementary pairing property of the DNA, the DNA nano structure can show good addressability.
Extended DNA nanostructures have been built in a repetitive arrangement from millions of building blocks, and in order to build addressable DNA nanostructures with more building blocks, the addressable components need to be repetitively arranged, and the overall size of the structure can be multiplied by the repetition level of the addressable strands.
Repeated use of addressable components can affect the addressable accuracy, in order to meet the requirements, technicians with abundant experience need to design a structure meeting the requirements through parameter adjustment on software in the design process of the DNA nano structure, the whole process is long in time consumption and complex in operation, and the technical barrier to designers is high. Therefore, research and development of an applicable rapid design method avoid conflict of repeatability and addressability, and have great significance for synthesis and application of DNA nano-structures.
While more hierarchies may result in larger structures, optimization of successive rounds of assembly procedures may be a daunting challenge. In recent years, the graph staining method has become more and more extensive in solving physical and biological problems, and thus is a very practical method for solving the addressable DNA polyhedron topology composed of repetitive components.
Disclosure of Invention
Aiming at the problems in the prior art, the invention aims to provide a graph dyeing and recombination method of an addressable DNA polyhedron topology, which can solve the problem of conflict between repeatability and addressability in the DNA polyhedron topology consisting of repeated components.
In order to solve the technical problems, the invention adopts the following technical scheme:
the invention provides a map staining method of an addressable DNA polyhedron topological structure, which comprises the following steps:
step 1, dyeing each edge of a DNA polyhedron by two colors, wherein the number of the edges of the two colors is equal, the edge of each color corresponds to an addressable component, and the addressable component comprises a first addressable component and a second addressable component;
step 2, synthesizing a DNA staining chain by using a plurality of the first addressable components and/or a plurality of the second addressable components, wherein the DNA staining chain corresponds to a number; a plurality of DNA staining chains correspond to a plurality of numbers one by one;
and 3, optimizing the plurality of DNA dyed chains to obtain the standard DNA dyed chains.
Further, in step 1, the DNA polyhedron is composed of n polygons, and each polygon is decomposed into m sides, wherein n is not less than 4 and n is an integer, m is not less than 3 and m is an integer.
Further, each side of each polygon comprises a first addressable component and a second addressable component according to the base complementary pairing rules.
Further, in step 2, one DNA dyed chain covers one face of the DNA polyhedron, and each DNA dyed chain includes the same number of addressable components as the number of edges of each face of the corresponding DNA polyhedron.
Furthermore, in step 3, the number of standard DNA staining strands is 2m-2, m is more than or equal to 3, and m is an integer.
The invention provides a recombination method of addressable DNA polyhedron topological structure, which comprises the following steps:
step 1, recombining DNA polyhedrons by utilizing DNA dyed chains to obtain a plurality of addressable DNA polyhedral topological structures, wherein the number corresponding to each DNA dyed chain of the addressable DNA polyhedral topological structures obtained by recombination can be correspondingly found in the faces of the addressable DNA polyhedral topological structures;
and 2, screening the addressable DNA polyhedron topological structure obtained by standard DNA dyed chain recombination from the plurality of addressable DNA polyhedron topological structures, wherein the addressable DNA polyhedron topological structure is the optimal addressable DNA polyhedron topological structure.
Further, the optimally addressable DNA polyhedron topology is an addressable DNA polyhedron topology that is recombined from two types of standard DNA dyed strands.
Further, each type of standard DNA-stained strand is a DNA-stained strand formed by alternating first addressable components and second addressable components.
Further, in the optimally addressable DNA polyhedron topology, the ratio of the number of two types of standard DNA stained strands is 1: 1.
Further, the addressable DNA polyhedron topology is a regular polyhedron or a convex polyhedron.
The invention can produce the beneficial effects that:
(1) the invention provides a graph dyeing and recombination method of an addressable DNA polyhedron topological structure, which is characterized in that each edge of each decomposed surface of a DNA polyhedron is dyed by two colors, each color corresponds to an addressable component, a plurality of first addressable components and/or a plurality of second addressable components are used for synthesizing a DNA dyed chain, the DNA dyed chain is optimized to obtain a standard DNA dyed chain, and the standard DNA dyed chain is recombined to obtain the addressable DNA polyhedron topological structure, so that the conflict between repeatability and addressability in the DNA polyhedron topological structure consisting of repeated components is avoided.
(2) The invention provides a map dyeing and recombination method of an addressable DNA polyhedron topological structure, which can rapidly, simply and qualitatively analyze an addressable recombination scheme of the DNA polyhedron topological structure consisting of repeated components, can quantitatively give the number of various DNA standard dyeing chains required in the scheme, can give a synthetic template of the qualitative and quantitative standard DNA dyeing chains without requiring experienced technicians to pay a large amount of time and energy, has accurate and reliable result, is easy to operate, is suitable for both a positive polyhedron and a convex polyhedron, and is suitable for wide popularization.
Drawings
FIG. 1 is a depiction and staining of addressable components in a regular tetrahedron, provided by an embodiment of the present invention;
FIG. 2 is a diagram illustrating the process of constructing and optimizing DNA dyed chains in regular tetrahedrons according to an embodiment of the present invention;
FIG. 3 is a schematic diagram of the topological structure of addressable DNA regular tetrahedrons based on standard stained strand recombination according to an embodiment of the present invention;
FIG. 4 is a schematic diagram of the topology of the optimally addressable DNA polyhedrons selected after regular dodecahedron staining according to an embodiment of the present invention.
Detailed Description
The present invention will be described in detail with reference to examples, but the present invention is not limited to these examples.
The addressable components which are repeatedly used are dyed by utilizing two colors, namely a color A and a color B respectively, then the addressable components are assembled into a standard dyeing chain according to rules, then the addressable DNA polyhedron topological structure is recombined by using the standard dyeing chain, the addressable DNA polyhedron topological structure formed by the two types of standard DNA dyeing chains in a weight ratio of 1:1 is the optimal addressable DNA polyhedron topological structure, and a theoretical template is provided for experimental synthesis.
Example 1
As shown in fig. 1, taking a DNA regular tetrahedron as an example, the DNA regular tetrahedron is composed of 4 regular triangles, each regular triangle is decomposed into 3 sides, and the 4 regular triangles are decomposed into 12 sides together.
Dyeing 12 sides by using a color A and a color B, wherein the number of the sides corresponding to the color A and the color B is equal, the color A has 6 sides, and the color B also has 6 sides, wherein the color A corresponds to a first addressable component, and the color B corresponds to a second addressable component;
as shown in fig. 2, a DNA-stained strand is synthesized using a plurality of first addressable modules and/or a plurality of second addressable modules, the DNA-stained strand corresponding to a number; the plurality of DNA dyed chains correspond to a plurality of numbers one by one, wherein the numbers can be numbers, letters and the like, and the numbers can be used as a mark for identifying the dyed chains;
specifically, a plurality of first addressable components and/or a plurality of second addressable components in the DNA regular tetrahedron can form 8 DNA staining chains, namely A-A-A, A-B-A, A-A-B, B-A-A, B-B-A, B-A-B, A-B-B and B-B-B, wherein A-A-A corresponds to the number 1, A-B-A corresponds to the number 2, A-A-B corresponds to the number 3, B-A-A corresponds to the number 4, B-B-A corresponds to the number 5, B-A-B corresponds to the number 6, A-B-B corresponds to the number 7, and B-B-B corresponds to the number 8, and 8 DNA staining chains are optimized, 4 standard DNA dyed chains are obtained, namely A-A-A, A-B-A, B-A-B and B-B-B, and the number corresponding to each standard DNA dyed chain is respectively A-A-A corresponding number 1, A-B-A corresponding number 2, B-A-B corresponding number 6 and B-B-B corresponding number 8.
As shown in fig. 3, the DNA polyhedrons were recombined using standard DNA dyed strands to obtain 4 addressable DNA polyhedron topologies, wherein the corresponding number of each DNA dyed strand recombined to obtain the addressable DNA polyhedron topology can be found in the face of the addressable DNA polyhedron topology; each side of each polygon comprises a first addressable component and a second addressable component according to the base complementary pairing principle; one DNA staining chain covers one face of the DNA regular tetrahedron, and the number of addressable components contained in each DNA staining chain is equal to the number of edges of each regular triangle of the corresponding DNA polyhedron, namely the number of the DNA staining chains covering each face of the DNA regular tetrahedron is 3;
as shown in fig. 3(a), from the 4 types of addressable DNA polyhedron topologies, the addressable DNA polyhedron topology recombined from two types of standard DNA dyed chains, i.e., a-B-a and B-a-B, is selected as the optimal addressable DNA polyhedron topology, wherein the number ratio of a-B-a and B-a-B in the optimal addressable DNA polyhedron topology is 1: 1.
Taking a DNA regular hexahedron as an example, each face of the DNA regular hexahedron is a regular quadrangle, decomposing 6 regular quadrangles into 24 sides in total, dyeing the 24 sides by using a color A and a color B to generate 12 first addressable components and 12 second addressable components, generating a plurality of DNA dyed chains by using a plurality of first addressable components and/or a plurality of second addressable components, optimizing the plurality of DNA dyed chains to obtain 6 standard DNA dyed chains,
in conclusion, the map dyeing and recombination method of the addressable DNA polyhedron topological structure provided by the invention is suitable for dyeing each side of a positive polyhedron to form a DNA dyed chain and a standard DNA dyed chain, the addressable DNA polyhedron topological structure can be constructed through the standard DNA dyed chain, and the problem of conflict between repeatability and addressability in the DNA polyhedron topological structure consisting of repeated components is solved.
Example 2
Taking a DNA regular dodecahedron as an example, the DNA regular dodecahedron is composed of 12 regular pentagons, each regular pentagon is decomposed into 5 sides, and the 12 regular pentagons are decomposed into 60 sides together.
Dyeing 60 edges by using a color A and a color B, wherein the number of the edges corresponding to the color A and the color B is equal, the color A has 30 edges, the color B has 30 edges, the color A corresponds to the first addressable component, and the color B corresponds to the second addressable component;
synthesizing a DNA-stained strand using the plurality of first addressable components and/or the plurality of second addressable components, the DNA-stained strand corresponding to a number; a plurality of DNA staining chains correspond to a plurality of numbers one by one;
and optimizing the plurality of DNA dyed chains to obtain standard DNA dyed chains, wherein the number of the standard DNA dyed chains is 8.
Recombining the DNA polyhedrons by utilizing the DNA dyed chains to obtain a plurality of addressable DNA polyhedral topological structures, wherein the number corresponding to each DNA dyed chain of the addressable DNA polyhedral topological structures obtained by recombination can be correspondingly found in the faces of the addressable DNA polyhedral topological structures; each side of each polygon comprises a first addressable component and a second addressable component according to the base complementary pairing rules. One DNA-dyed strand covers one face of the DNA polyhedron, and each DNA-dyed strand contains the same number of addressable components as the number of edges of each face of the corresponding DNA polyhedron.
Screening addressable DNA polyhedron topologies obtained by recombining standard DNA dyed chains from a plurality of addressable DNA polyhedron topologies, namely, the optimal addressable DNA polyhedron topologies, wherein the optimal addressable DNA polyhedron topologies are two, as shown in FIG. 4, the first optimal addressable DNA polyhedron topology is obtained by recombining two types of standard DNA dyed chains, the two types of standard DNA dyed chains are A-A-A-B-B and B-B-B-A-A, respectively, wherein the number ratio of A-A-A-B-B-B and B-B-B-A-A in the optimal addressable DNA polyhedron topologies is 1: 1; the second most optimally addressable DNA polyhedron topology is recombined from two types of standard DNA dyed strands, A-B-A-B-A and B-A-B-A-B, respectively, where the number ratio of A-B-A-B-A and B-A-B-A-B in the optimally addressable DNA polyhedron topology is 1: 1.
Wherein, convex polyhedron means that any one face of polyhedron is extended into plane, if all other faces are on the same side of this plane, and regular dodecahedron is also convex polyhedron, therefore, the map dyeing and recombination method of addressable DNA polyhedron topological structure disclosed by this invention is suitable for convex polyhedron too.
The invention provides a map dyeing and recombination method of an addressable DNA polyhedron topological structure, which is characterized in that each edge of each decomposed surface of a DNA polyhedron is dyed by two colors, each color corresponds to an addressable component, a plurality of first addressable components and/or a plurality of second addressable components are utilized to synthesize a DNA dyed chain, the DNA dyed chain is optimized to obtain a standard DNA dyed chain, and then the addressable DNA dyed chain is recombined to obtain the addressable DNA polyhedron topological structure, so that the conflict between repeatability and addressability in the DNA polyhedron topological structure consisting of repeated components is avoided, the method can rapidly, simply and qualitatively analyze the recombination scheme of the addressable DNA polyhedron topological structure consisting of repeated components, simultaneously can quantitatively give the number of various DNA standard dyed chains required in the scheme, and does not need to require a great deal of time and energy of skilled technicians, the method can provide a qualitative and quantitative synthetic template of the standard DNA dyed chain, has accurate and reliable result, is easy to operate, is suitable for both regular polyhedrons and convex polyhedrons, and is suitable for wide popularization.
Although the present application has been described with reference to a few embodiments, it should be understood that various changes, substitutions and alterations can be made herein without departing from the spirit and scope of the application as defined by the appended claims.
Claims (10)
1. A method for map staining of addressable DNA polyhedron topology comprising the steps of:
step 1, dyeing each edge of a DNA polyhedron by two colors, wherein the number of the edges of the two colors is equal, the edge of each color corresponds to an addressable component, and the addressable component comprises a first addressable component and a second addressable component;
step 2, synthesizing a DNA staining chain by using a plurality of the first addressable components and/or a plurality of the second addressable components, wherein the DNA staining chain corresponds to a number; a plurality of DNA staining chains correspond to a plurality of numbers one by one;
and 3, optimizing the plurality of DNA dyed chains to obtain the standard DNA dyed chains.
2. The method for map-staining addressable DNA polyhedrons topology according to claim 1, characterized in that in step 1, said DNA polyhedrons are composed of n polygons, each of said polygons is decomposed into m sides, where n ≧ 4 and n are integers, m ≧ 3 and m are integers.
3. The method for map staining of addressable DNA polyhedron topology according to claim 2, characterized in that each side of each polygon contains one first addressable component and one second addressable component according to the base complementary pairing rules.
4. The method for map-staining addressable DNA polyhedra topology according to claim 1 wherein in step 2, one DNA-stained strand covers one face of a DNA polyhedron and each DNA-stained strand contains the same number of addressable components as the number of edges of each face of the corresponding DNA polyhedron.
5. The method for map-staining addressable DNA polyhedra topology according to claim 1, characterized in that in step 3 the number of standard DNA stained strands is 2m-2, m ≧ 3 and m is an integer.
6. A method of recombining an addressable DNA polyhedron topology, comprising the steps of:
step 1, recombining DNA polyhedrons by utilizing DNA dyed chains to obtain a plurality of addressable DNA polyhedral topological structures, wherein the number corresponding to each DNA dyed chain of the addressable DNA polyhedral topological structures obtained by recombination can be correspondingly found in the faces of the addressable DNA polyhedral topological structures;
and 2, screening the addressable DNA polyhedron topological structure obtained by standard DNA dyed chain recombination from the plurality of addressable DNA polyhedron topological structures, wherein the addressable DNA polyhedron topological structure is the optimal addressable DNA polyhedron topological structure.
7. The method of recombining an addressable DNA polyhedron topology according to claim 6, wherein the optimal addressable DNA polyhedron topology is an addressable DNA polyhedron topology recombined from two types of standard DNA dyed strands.
8. The method for reorganization of addressable DNA polyhedron topology according to claim 6, wherein each type of standard DNA stained strand is DNA stained chain formed by alternating first addressable module and second addressable module.
9. The method of recombining an addressable DNA polyhedron topology according to claim 7, wherein in the optimally addressable DNA polyhedron topology the ratio of the number of two types of standard DNA dyed strands is 1: 1.
10. The method of reorganization of an addressable DNA polyhedron topology according to claim 6, wherein said addressable DNA polyhedron topology is a regular polyhedron or a convex polyhedron.
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Citations (2)
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| CA2263716A1 (en) * | 1997-06-12 | 1998-12-17 | Sloan-Kettering Institute For Cancer Research | Covalent joining of dna strands to rna strands catalyzed by vaccinia topoisomerase |
| CN109558654A (en) * | 2018-11-15 | 2019-04-02 | 北京科技大学 | A kind of plane tension integral structure topology design method |
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Patent Citations (2)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CA2263716A1 (en) * | 1997-06-12 | 1998-12-17 | Sloan-Kettering Institute For Cancer Research | Covalent joining of dna strands to rna strands catalyzed by vaccinia topoisomerase |
| CN109558654A (en) * | 2018-11-15 | 2019-04-02 | 北京科技大学 | A kind of plane tension integral structure topology design method |
Non-Patent Citations (2)
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| JINWEI DUAN等: "Rational design of DNA platonic polyhedra with the minimal components number from topological perspective", IOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, pages 2 - 4 * |
| 程晓胜;陈小艳;: "一类双交叉多面体链环模型的分支数与手性", 湖北师范学院学报(自然科学版), no. 02 * |
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