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Method for preparing oligonucleotide chip in use for DNA surface computer in heterozygosis with computer

An oligonucleotide and surface computing technology, which is applied in the field of preparation of oligonucleotide chips for DNA surface computing, can solve the problems of increasing variable operation, inability to use, errors, etc., and achieves simple operation process and reduced false positive rate. Effect

Inactive Publication Date: 2005-08-31
SHANGHAI JIAO TONG UNIV
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  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

Although this work uses a computing chip, because the encoding method adopted in the algorithm design is that the sequences of the corresponding state codes of n variables are sequentially connected, the number of variables increases, the length of the sequence increases, and the synthesis of too long sequences (greater than 120bp ) will become a big obstacle, and the calculation process involves multiple enzyme operations, which will cause large errors when increasing the variable operation. In addition, this calculation chip and its calculation mode are only suitable for SAT problem calculations and cannot be used for Calculations for other NP problems

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  • Method for preparing oligonucleotide chip in use for DNA surface computer in heterozygosis with computer
  • Method for preparing oligonucleotide chip in use for DNA surface computer in heterozygosis with computer
  • Method for preparing oligonucleotide chip in use for DNA surface computer in heterozygosis with computer

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Embodiment 1

[0029] A DNA surface computing chip for solving SAT problems hybridized with computer computing

[0030] The present invention is an example with a SAT problem of 4 variables, and this problem is described as:

[0031] F=(w∨x∨y)∧(w∨y∨z)∧(x∨y)∧(w∨y)

[0032] Find the values ​​of the four variables when F=1

[0033] The steps of DNA surface calculation chip design and hybrid calculation of this problem with electronic computer are described as follows:

[0034] (1) Generate a DNA surface computing chip

[0035] ① The SAT question contains 4 variables (w, x, y, z) and 4 clauses, each variable takes a value of 1 or 0, then the complete data pool of the question contains 2 4 = 16 data, arranged in the order of wxyz, the 16 data are as follows: 0000, 0001, 0010, 0011, 0100, 0101, 0110, 0111, 1000, 1001, 1010, 1011, 1100, 1101, 1110, 1111

[0036] x

[0037] 0 0

[0038] variable value

[0039] The oligonucleotide chain encoded by the above SAT pr...

Embodiment 2

[0048] DNA Surface Computing Chip for Solving the Maximum Clique Problem Hybridized with Computer Computing

[0049] A group of a graph G is a vertex subset S of the graph G, so that there is an edge connection between any two vertices in S. If there is |S|≥|S′| for any other group S′ of G, it is called S is the largest clique of G. The maximum clique problem of a graph is an NP-complete problem.

[0050] The present invention takes a given graph with 6 vertices as an example. The given figure is attached Figure 3a , manually draw its complement as attached Figure 3b .

[0051] The steps of DNA surface calculation chip design and hybrid calculation of this problem with electronic computer are described as follows:

[0052] (1) Generate a DNA surface computing chip

[0053] ① The maximum clique problem contains 6 vertices. First, define a mapping strategy for a complete data pool:

[0054] a. Vertices are represented by A1, A2, A3, A4, A5, and A6 respectively.

[0055...

Embodiment 3

[0073] A DNA surface computing chip for solving the maximum vertex segmentation problem of graphs hybridized with computer computing. The maximum vertex segmentation problem of a graph is, given a graph G, there is a subset S of vertices in graph G, and the total number of connecting lines between any vertex in S and vertices outside the subset is the largest, then this vertex The subset is the maximum vertex split for a given graph G. This is also an NP-complete problem.

[0074] The present invention takes a given graph with 6 vertices as an example, and the given graph is as attached Figure 5 .

[0075] The model and steps of the DNA computing chip to calculate this problem are as follows:

[0076] (1) Generate a DNA surface computing chip

[0077] ① The maximum vertex segmentation problem contains 6 vertices. First, define a mapping strategy for a complete data pool:

[0078] a There are two assignments for setting Ai, when the vertex is in the vertex subset, the val...

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Abstract

A process for preparing oligonucleotide chip used in DNA surface calculation to solve the NP question is disclosed, which features that the coding and arranging of the oligonucleotide sequenes on DNA surface calculation chip are in such manner that the data in data pool is converted to the binary form, the data pool is converted to an array, and each data in the array is mapped to an oligonucleotide sequence, that is, a point on the chip.

Description

technical field [0001] The invention relates to a preparation method used in the technical field of DNA chips, in particular to a preparation method of an oligonucleotide chip for computing a DNA surface hybridized with a computer. Background technique [0002] In 1994, Adleman (Science, 1994, 266: 1021-1024) used DNA sequence as the information carrier for the first time, and used molecular biology test technology to solve an NP-complete problem (Hamilton path problem with seven vertices) in a test tube, and pointed out that DNA molecules The calculation has the characteristics of high information degree and high parallelism, so that it can solve difficult problems such as NP-complete problems in linear time. If these NP-complete problems are solved by Turing machines, the time required is exponentially increasing. After Adleman, many scholars proposed a variety of DNA computing models for different NP problems, involving SAT problems, maximum clique problems, maximum inde...

Claims

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Application Information

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IPC IPC(8): C12Q1/68G06F7/00
Inventor 张晓东吴凝潘加奎张素胡钧张治洲
Owner SHANGHAI JIAO TONG UNIV
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