Oligonucleotide series for calculation of DNA chip

An oligonucleotide and computing chip technology, applied in the field of oligonucleotide sequences, can solve the problems of poor hybridization stability, unable to guarantee hybridization stability at the same time, no hybridization mismatch, weak signal, etc.

Inactive Publication Date: 2005-08-24
SHANGHAI JIAO TONG UNIV
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

However, for the hybridization reaction on the surface of the chip, due to the requirement of the hybridization stability of the oligonucleotide sequence, the sequence length usually needs to exceed 12 bases. If it is lower than this length, the hybridization stability is poor

Method used

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  • Oligonucleotide series for calculation of DNA chip

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0049]12-base variable parent sequence (n=22) pairing test results (comparison scores are expressed in matrix arrangement):

[0050] 01

[0051] 01

[0052] In the summary of the invention, the constraint condition (4) "the alignment score between the complete complementary sequences of any sequence A and any sequence B (A, B can be the same)" test results:

[0053]

[0054] 14

[0055] The above test results show that the selected 22 sequences all meet the constraint conditions (3) and (4) in the content of the invention in the description, that is, the comparison scores are not greater than 4.

Embodiment 2

[0057] A 4-variable SAT problem is encoded with the parent sequence, and arranged as a computing chip.

[0058] For a 4-variable SAT problem such as

[0059] F=(w∨x∨y)∧(w∨y∨z)∧(x∨y)∧(w∨y)

[0060] gcagtatccaca aggaactgagct

[0061] variable value

[0062] Z＝0

[0063] The steps for the DNA computing chip to calculate this problem are as follows:

[0064] (1) Generate a DNA surface computing chip

[0065] 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 order of wxyz, 16 data are as follows: 0000, 0001, 0010, 0011, 0100, 0101, 011O, 0111, 1000, 1001, 1010, 1011, 1100, 1101, 1110, 1111

[0066] x

[0067] 0 0

[0068] ② Arrange the oligonucleotide sequences encoding the 8 states of the 4 variables of the above SAT problem on the chip according to the above array format to obtain an ...

Embodiment 3

[0074] The same 4-variable SAT problem as in Example 2 is encoded with the extended sequence, and arranged as a computing chip.

[0075] First pair: cagactagcctt aaggctagtctg

Second pair: ctctgattcgtc gacgaatcagag

Third pair: caaggacatacg cgtatgtccttg

Fourth pair: tcgctaaagggt accctttagcga

[0076] variable value

Sequence immobilized on chip (5'-3')

Fully paired probes (5'-3')

X＝1

NH 2 -AAA AAA AAA AAA AAA cagactagcctt

FAM-aaggctagtctg

X＝0

NH 2 -AAA AAA AAA AAA AAA aaggctagtctg

FAM-cagactagcctt

Y＝1

NH 2 -AAA AAA AAA AAA AAA ctctgattcgtc

FAM-gacgaatcagag

Y＝0

NH 2 -AAA AAA AAA AAA AAA gacgaatcagag

FAM-ctctgattcgtc

[0077] Z＝1

NH 2 -AAA AAA AAA AAA AAA caaggacatacg

FAM-cgtatgtccttg

Z＝0

NH 2 -AAA AAA AAA AAA AAA cgtatgtccttg

FAM-caaggacatacg

W＝1

NH 2 -AAA AAA AAA AAA AAA tcgctaa...

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Abstract

A group of oligonucleotide sequences used for the calculation of DNA chip features that the length of its each sequence is 12 bases, and its each sequence can meet such restrictive conditions that 22 mother sequences are generated, the content of G+C is 90%, and the ratio of any sequence to another sequence is not greater than 4.

Description

technical field [0001] The present invention relates to an oligonucleotide sequence in the field of gene technology, in particular to an oligonucleotide sequence used in a DNA computing chip. Background technique [0002] DNA computing is a new field developed in recent years. 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 the Hamilton path problem of the seven vertices in the test tube. Later, many scholars proposed a variety of DNA calculation models for different NP problems, and these DNA calculations are all calculations in the solution system. Although a variety of DNA calculations can be realized in the solution, there are still some insurmountable problems in the reaction in the solution, such as the difficulty of separating intermediate products, the complexity of the reaction system, the difficulty of monitoring the intermediate process, the poor ...

Claims

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Application Information

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IPC IPC(8): C12N15/00
Inventor 张晓东吕鸣胡钧贺林张治洲
Owner SHANGHAI JIAO TONG UNIV
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