CN107437003B

CN107437003B - Probe machine implementation method and device based on DNA calculation

Info

Publication number: CN107437003B
Application number: CN201710581927.2A
Authority: CN
Inventors: 许进; 石晓龙; 李生辉; 陈从周
Original assignee: Peking University
Current assignee: Peking University
Priority date: 2017-07-17
Filing date: 2017-07-17
Publication date: 2021-03-23
Anticipated expiration: 2037-07-17
Also published as: CN107437003A

Abstract

The embodiment of the invention provides a method and a device for realizing a probe machine based on DNA calculation. The method comprises the steps of obtaining preset conditions according to a mathematical problem to be solved, and respectively carrying out DNA sequence coding on a DNA origami structure and a DNA single chain according to the preset conditions; constructing a database comprising the DNA origami structure; constructing a probe library comprising the DNA single strands; carrying out mixed reaction on the DNA origami structure and the DNA single strand on a computing platform to obtain a reaction product; the reaction product is detected by a detector to obtain a calculation result. The embodiment of the invention utilizes the DNA origami structure and the DNA single strand in the DNA calculation to form the probe machine, thereby improving the processing capacity of the computer, facilitating the detection of the calculation result, effectively improving the problem of larger mismatching rate of the self-assembly of the traditional algorithm, improving the reliability of the calculation result, and realizing the random communication and specific assembly of data in a three-dimensional space.

Description

Probe machine implementation method and device based on DNA calculation

Technical Field

The embodiment of the invention relates to the technical field of biological computers, in particular to a method and a device for realizing a probe machine based on DNA calculation.

Background

In the development process of the electronic computer, the electronic computer always follows the moore's law, and makes great contribution to the development of the human civilization society. However, the development of electronic computers has now met with significant obstacles. There are two main points: first, the technology of manufacturing electronic computers is reaching its limits. Second, electronic computers have not been able to handle the large-scale NP-complete problem due to the turing model.

Due to the principle of base complementary pairing peculiar to DNA molecules and the superior structural characteristics thereof, the DNA molecule is particularly suitable to be used as an element of a structural system. The DNA molecule is a typical substance with nanometer scale, the structural unit of the DNA molecule is stable and flexible, the coding property is good, the operability is strong, and the biological technology based on the DNA molecule is mature day by day. DNA computing has attracted a number of laboratories worldwide for relevant research from the point of presentation to today. Currently, DNA computation can be divided into general computation and logic gate computation. Logic gate calculations are based on DNA single strand displacement to achieve input and output, both of which are DNA single strands. The common calculation is based on the complementary formation of macromolecular structures by DNA single-stranded bases, such as the traveler problem realized by Adleman, the SAT problem realized by Lipton, the chess problem realized by Landweber, and the like.

The DNA single-strand is taken as a main body to realize mutual reaction, the calculation result is a large group of DNA strands, the result must be read through sequencing, the process is complicated, or the molecular weight detection is qualitatively determined by means of running glue and the like, and the reliability is low and is not intuitive.

Disclosure of Invention

The embodiment of the invention provides a method and a device for realizing a probe machine based on DNA (deoxyribonucleic acid) calculation, which are used for solving the defects that the traditional computer in the prior art is not high enough in calculation efficiency, complicated in result detection process, low in reliability and unintuitive.

In one aspect, the present invention provides a probe machine implementation method based on DNA calculation, including:

acquiring preset conditions according to a mathematical problem to be solved, and respectively carrying out DNA sequence coding on the DNA origami structure and the DNA single strand according to the preset conditions;

constructing a database comprising the DNA origami structure;

constructing a probe library comprising the DNA single strands;

carrying out mixed reaction on the DNA origami structure and the DNA single strand on a computing platform to obtain a reaction product;

the reaction product is detected by a detector to obtain a calculation result.

In another aspect, an embodiment of the present invention provides a probe machine implementation apparatus based on DNA calculation, including:

the programming module is connected with the database and the probe library and is used for acquiring preset conditions according to the mathematical problem to be solved and respectively carrying out DNA sequence coding on the DNA paper folding structure and the DNA single strand according to the preset conditions;

the database is used for storing the DNA paper folding structure;

the probe library is used for storing the DNA single strand;

the calculation platform is connected with the database, the probe library and the detector and is used for carrying out mixed reaction on the DNA origami structure and the DNA single strand on the calculation platform to obtain a reaction product;

the detector is used for detecting the reaction product to obtain a calculation result.

According to the method and the device for realizing the probe machine based on the DNA calculation, the setting of the probe machine is realized by utilizing the DNA paper folding structure and the DNA single strand of the DNA calculation, the calculation efficiency of a computer is improved, and the calculation result is easy to detect.

Drawings

FIG. 1 is a schematic flow chart of a DNA calculation-based probe machine implementation method according to an embodiment of the present invention;

FIG. 2 is a schematic view of the coloring structure of the DNA origami structure according to the embodiment of the present invention;

FIG. 3 is a schematic diagram of a 6 vertex 3 coloring problem according to an embodiment of the present invention;

FIG. 4 is a schematic diagram of a 6 vertex 3 coloring problem calculation result structure according to an embodiment of the present invention;

FIG. 5 is a schematic structural diagram of a DNA calculation-based probe machine implementation apparatus according to an embodiment of the present invention.

Detailed Description

In order to make the objects, technical solutions and advantages of the embodiments of the present invention clearer, the technical solutions in the embodiments of the present invention will be clearly and completely described below with reference to the drawings in the embodiments of the present invention, and it is obvious that the described embodiments are some, but not all, embodiments of the present invention. All other embodiments, which can be derived by a person skilled in the art from the embodiments given herein without making any creative effort, shall fall within the protection scope of the present invention.

FIG. 1 is a schematic flow chart of a DNA calculation-based probe machine implementation method according to an embodiment of the present invention, as shown in FIG. 1, the method includes:

step S01, acquiring preset conditions according to the mathematical problem to be solved, and respectively carrying out DNA sequence coding on the DNA paper folding structure and the DNA single strand according to the preset conditions;

when a traditional computer is used for solving a mathematical problem, a corresponding program is required to be edited according to the mathematical problem to be solved, and then the program is operated to perform calculation on the mathematical problem to be solved.

The prober that is to be implemented by the embodiments of the present invention is also a computer model in nature, and therefore, it is also necessary to perform a programming operation before calculating the mathematical problem to be solved. The method comprises the following steps of firstly obtaining corresponding preset conditions through the mathematical problem to be solved, and then using tools such as a computer to assist in analyzing and designing a DNA origami structure and a DNA base pair sequence of a DNA single strand according to the preset conditions.

Step S02, constructing a database comprising the DNA origami structure;

step S03, constructing a probe library including the DNA single strand;

step S02 and step S03 are not sequentially performed, and practical applications may be determined as appropriate, in the embodiment of the present invention, only step S02 is performed before step S03 is performed after step S03, and other implementation manners will not be described again.

All the DNA origami structures obtained by the above analysis and design are stored in a database, and all the DNA single strands obtained by the above analysis and design are put in a probe library at the same time. The database and the probe library are containers filled with certain buffer solution, wherein the containers respectively contain the DNA origami structures and the DNA single strands, and the number of the structures can reach 10 trillion/ml.

Step S04, carrying out mixed reaction on the DNA paper folding structure and the DNA single strand on a computing platform to obtain a reaction product;

and mixing the DNA origami structure contained in the database and the DNA single strand contained in the probe library into a computing platform according to a certain proportion, wherein the computing platform is a container filled with a certain buffer solution, and the certain proportion can be adjusted correspondingly according to actual needs. At the moment, the DNA origami structure and the DNA single strand in the computing platform can continuously move in the computing platform at the molecular thermal movement speed in the liquid by adjusting the reaction environment of the computing platform. The DNA origami structure and the DNA single strand are automatically connected with each other according to the base pairing principle through molecular acting force and hydrogen bonds to realize algorithm self-assembly. Over a period of time, such as three days, a week or even weeks, the final reaction product is left in the computing platform.

And step S05, detecting the reaction product through a detector to obtain a calculation result.

Because there is a certain random factor in the ligation process of the DNA origami structure and the DNA single strand, there are some undesired calculation results, so-called non-solutions, in addition to the desired calculation result, so-called true solution, and some DNA origami structure and DNA single strand which are not successfully ligated in the reaction product. At this time, a detector is needed to detect the reaction product left in the computing platform, and the desired computing result of the mathematical problem to be solved is selected according to the preset detection condition.

Further, the detector is an atomic force microscope.

There are many detectors for detecting the reaction product, such as an atomic force microscope, through which the connection condition between each DNA origami structure and DNA single strand in the reaction product can be visually observed, and through setting the atomic force microscope, some desired specific connection relationships can be extracted, and the number of the specific connection relationships can be visually calculated, and even a dynamic video of the connection (calculation process) can be photographed. Of course, the particular detector used may be selected according to the actual application.

According to the embodiment of the invention, through the analysis of the mathematical problem to be solved, a database containing a corresponding DNA origami structure and a probe library containing a corresponding DNA single strand are constructed, the two parts are subjected to mixed reaction on a computing platform, and finally, a reaction product is detected through a detector, so that the final computing result is obtained. The method can improve the calculation efficiency of the computer on the mathematical problem to be solved, and is easy to detect the calculation result. The problem of large mismatching rate of self-assembly of the traditional algorithm can be effectively solved, the reliability of a calculation result is improved, data can be randomly exchanged in a three-dimensional space, and the data are specifically assembled.

Based on the above embodiment, further, the DNA origami structure is a double-layer structure, and a corresponding number of connecting arms are extended according to the preset condition.

In the traditional DNA calculation, a two-dimensional DNA structure is mostly adopted, the DNA paper folding technology is proposed by the California Ritemund in 2006, and at present, the DNA paper folding technology is mostly used at home and abroad to make structures, such as a triangle, a quadrangle, a pentagram structure, a map and the like, and the operation on a two-dimensional plane is determined when the DNA paper folding technology is originally designed. The technology is mainly used in the aspects of medical nano drug loading, force curve and spectrum measurement in physics and the like. These two-dimensional structures do not meet the requirements of the prober for three-dimensional structures in the database.

The DNA paper folding structure designed in the embodiment of the invention is a double-layer structure, a corresponding number of connecting arms can be freely extended out of the surface of the structure according to the preset conditions, and the connecting arms can be rotated at any position in a three-dimensional space, so that the DNA paper folding structure can be specifically connected with a DNA single chain in the three-dimensional space according to a base pairing principle, and the limitation of two-dimensional plane connection is overcome. Meanwhile, due to the existence of the connecting arm, the DNA paper folding structure connected together through the DNA single strands is easier to clearly observe and obtain by a detector. In addition, the connecting arm can also flick other DNA paper folding structures, so that the mutual accumulation force between the two-dimensional DNA paper folding structures is avoided.

According to the embodiment of the invention, the DNA paper folding structure contained in the database is designed into a double-layer structure, and a certain number of connecting arms extend out, so that the applicability of the DNA paper folding structure to the realization of a probe machine is enhanced, the limitation of the DNA paper folding structure is overcome, the visualization of the calculation result of the probe machine is realized, the problem of high mismatching rate of the self-assembly of the traditional algorithm can be effectively improved, the reliability of the calculation result is improved, and the data can be arbitrarily exchanged and specifically assembled in a three-dimensional space.

Based on the above embodiment, further, the DNA origami structure and the DNA single strand are mixed and reacted on a computing platform to obtain a reaction product, specifically,

and putting the DNA origami structure and the DNA single strand into a TAE buffer solution for mixed dissolution, and accurately controlling the temperature by using PCR.

In the practical application process, after the mathematical problem to be solved is analyzed, DNA origami structures and DNA single-stranded DNA sequences are designed, and corresponding DNA origami structures and DNA single-stranded samples are ordered to professional commercial companies according to the generated DNA sequences. The obtained sample is centrifuged and then prepared into a certain concentration, for example, 10umol/L, by using TAE buffer solution, and then subpackaged and marked, namely a database and a probe library are constructed. The DNA synthesis reporter attached to the sample is labeled with concentrations such as: 10D ≈ 0.0035umol one tube with a package amount of 1 OD. Selecting proper TAE buffer solution to dissolve, and mixing the DNA origami structures and DNA single strands in the database and the probe library according to a certain proportion. The precise control of the annealing temperature, for example, the setting of the gradient annealing temperature and time using a PCR apparatus, enables the efficient control of the production efficiency, that is, the result of the calculation, wherein the temperature and time can be set according to the length of the DNA sequence to be produced.

According to the embodiment of the invention, the DNA paper folding structure and the DNA single strand are placed into the TAE buffer solution for mixing and dissolving, and the PCR precise temperature control is used, so that the aim of flexibly controlling the generation efficiency of the reaction product of the DNA paper folding structure and the DNA single strand is achieved, and the efficient operation of a probe model computer is realized.

Fig. 2 is a schematic view of a coloring structure of the DNA origami structure according to an embodiment of the present invention, and as shown in fig. 2, the DNA origami structure is colored and marked according to the preset condition.

In order to enable the reaction product to be clearly observed by a detector, for example, an atomic force microscope, thereby obtaining a calculation result, the DNA origami structure is color-labeled according to the preset condition. The label can be Arabic data "1", "2", "3" or Roman numerals "I", "II", "III", etc., or can be rectangle, two columns and "T" shape as shown in FIG. 2, at this time, the DNA origami structure observed by atomic force microscope will be shown in the lower part of FIG. 2, and three different colored shapes can be clearly distinguished. The specific mark can be adjusted according to the actual requirement.

There are many methods for marking, for example: nanogold-thiolated oligonucleotide, biotin-streptavidin, and a fluorophore.

According to the embodiment of the invention, the DNA origami structure can be distinguished by directly observing under a detector through coloring and marking the DNA origami structure, so that the calculation result is easy to detect.

Based on the above embodiment, the 6-vertex 3 coloring problem will be specifically exemplified below.

Fig. 3 is a schematic structural diagram of a 6-vertex 3 coloring problem according to an embodiment of the present invention, and fig. 4 is a schematic structural diagram of a calculation result of the 6-vertex 3 coloring problem according to the embodiment of the present invention. As shown in fig. 3, the 6-point can only be colored three colors of red, blue and yellow. The known condition is that the colors of the vertexes No. 1, No. 2 and No. 3 are red, yellow and blue respectively, and the coloring of the vertexes No. 4, No. 5 and No. 6 is solved, so that all solutions with different coloring of the two connected vertexes are obtained.

Based on the proposed problems and known conditions, DNA sequences are designed and DNA coding is performed to obtain a database containing DNA origami structures and a probe library containing DNA single strands after coding. Since the mathematical problem to be solved is three-colored, three markers are designed on the DNA origami structure, as shown in fig. 2. From the problems of 6-vertex 3 staining, conditions are known, and in the corresponding mathematical model, there are 14 possible combinations of DNA origami structures and DNA single strands, and thus there are 14 types of probe libraries. The computer aided design of 14 kinds of DNA single strands can ensure the mutual connection specificity.

The operation platform puts a database and a probe library together in a TAE solution, and obtains a reaction product by using PCR (polymerase chain reaction) accurate temperature control, namely a reaction solving process.

As shown in fig. 4, the solved reaction product was subjected to detection analysis using an atomic force microscope. The result of the calculation will have many non-solutions beyond the desired solution that may not be justified. However, the solution is correct as long as the structure has 6 vertices. So one calculation yields all positive solutions.

FIG. 5 is a schematic structural diagram of a DNA calculation-based probe machine implementation apparatus according to an embodiment of the present invention, as shown in FIG. 5, the apparatus includes: a programming module 11, a database 12, a probe library 13, a computing platform 14, and a detector 15, wherein,

the programming module 11 is connected with the database 12 and the probe library 13, and is used for acquiring preset conditions according to a mathematical problem to be solved, and respectively carrying out DNA sequence coding on the DNA origami structure and the DNA single strand according to the preset conditions; the database 12 is used for storing the DNA origami structure; the probe pool 13 is used for storing the DNA single strand; the computing platform 14 is connected with the database 12, the probe library 13 and the detector 15, and is used for performing mixed reaction on the DNA origami structure and the DNA single strand on the computing platform 14 to obtain a reaction product; the detector 15 is configured to detect the reaction product to obtain a calculation result.

Specifically, the programming module 11 first obtains the corresponding preset conditions through the mathematical problem to be solved, and then, according to the preset conditions, may assist in analyzing and designing the DNA origami structure and the DNA base pair sequence of the DNA single strand by using tools such as a computer.

All the DNA origami structures obtained by the above analysis and design are stored in the database 12, and all the DNA single strands obtained by the above analysis and design are put in the probe library 13. Wherein the database 12 and the probe library 13 are specifically containers filled with a buffer solution, and the containers respectively contain the DNA origami structure and the DNA single strand.

The DNA origami structure contained in the database 12 and the DNA single strand contained in the probe library 13 are mixed into the computing platform 14 according to a certain ratio, wherein the computing platform 14 is specifically a container filled with a certain buffer solution, and the certain ratio can be adjusted according to actual needs. At this time, the reaction conditions of the computing platform 14 are adjusted to make the DNA origami structure and DNA single strand move continuously in the computing platform at the moving speed of the thermal motion of the molecules in the liquid. The DNA origami structure and the DNA single strand are automatically connected with each other according to the base pairing principle through molecular acting force and hydrogen bonds to realize algorithm self-assembly. The reaction over time leaves the final reaction product in the computing platform 14.

Because there is a certain random factor in the ligation process of the DNA origami structure and the DNA single strand, there are some undesired calculation results, so-called non-solutions, in addition to the desired calculation result, so-called true solution, and some DNA origami structure and DNA single strand which are not successfully ligated in the reaction product. In this case, a detector 15 is required to detect the reaction product left in the computing platform, and the desired calculation result of the mathematical problem to be solved is selected according to the preset detection condition.

Further, the detector 15 is an atomic force microscope.

The apparatus provided in the embodiment of the present invention is configured to execute the method, and the functions of the apparatus refer to the method embodiment specifically, and detailed method flows thereof are not described herein again.

In the embodiment of the invention, the programming module 11 is used for analyzing the mathematical problem to be solved, a database 12 containing a corresponding DNA origami structure and a probe library 13 containing a corresponding DNA single strand are constructed, the two parts are subjected to mixed reaction on a computing platform 14, and finally, a reaction product is detected by a detector 15, so that the final computing result is obtained. The method can improve the calculation efficiency of the computer on the mathematical problem to be solved, and is easy to detect the calculation result.

According to the embodiment of the invention, the DNA paper folding structure contained in the database is designed into a double-layer structure, and a certain number of connecting arms extend out, so that the applicability of the DNA paper folding structure to the implementation of a probe machine is enhanced, the limitation of the DNA paper folding structure is overcome, and the visualization of the calculation result of the probe machine is realized.

Based on the above embodiment, further, the DNA origami structure is color-labeled according to the preset condition.

In order to enable the reaction product to be clearly observed by a detector, for example, an atomic force microscope, thereby obtaining a calculation result, the DNA origami structure is color-labeled according to the preset condition. The mark can be rectangular, two columns and T-shaped as shown in FIG. 2, and the DNA origami structure observed by an atomic force microscope is shown in the lower part of FIG. 2, so that three different colored shapes can be clearly distinguished. The specific mark can be adjusted according to the actual requirement.

Finally, it should be noted that: the above examples are only intended to illustrate the technical solution of the present invention, but not to limit it; although the present invention has been described in detail with reference to the foregoing embodiments, it will be understood by those of ordinary skill in the art that: the technical solutions described in the foregoing embodiments may still be modified, or some technical features may be equivalently replaced; and such modifications or substitutions do not depart from the spirit and scope of the corresponding technical solutions of the embodiments of the present invention.

Claims

1. A method for implementing a probe machine based on DNA calculation is characterized by comprising the following steps:

constructing a database comprising the DNA origami structure;

constructing a probe library comprising the DNA single strands;

detecting the reaction product by a detector to obtain a calculation result;

the DNA paper folding structure is a double-layer structure, and a corresponding number of connecting arms are extended out according to the preset conditions.

2. The method according to claim 1, wherein the DNA origami structure and the DNA single strand are subjected to a mixed reaction on a computing platform to obtain a reaction product, in particular,

3. The method of claim 1, wherein the detector is an atomic force microscope.

4. The method according to claim 1, wherein the DNA origami structure is color-labeled according to the preset condition.

5. A DNA computation-based prober implemented apparatus, comprising:

the programming module is connected with the database and the probe library and used for acquiring preset conditions according to the mathematical problem to be solved and respectively carrying out DNA sequence coding on the DNA paper folding structure and the DNA single strand according to the preset conditions;

the database is used for storing the DNA paper folding structure;

the probe library is used for storing the DNA single strand;

the detector is used for detecting the reaction product to obtain a calculation result;

6. The apparatus according to claim 5, wherein the DNA origami structure and the DNA single strand are subjected to a mixed reaction on a computing platform to obtain a reaction product, in particular,

7. The apparatus of claim 5, wherein the detector is an atomic force microscope.

8. The apparatus according to claim 5, wherein the DNA origami structure is color-labeled according to the preset condition.