A DNA Network Construction Method Based on Strand Displacement Regulation of E6 Ribozyme Function

A construction method and strand replacement technology, applied in the field of biological computing, can solve problems such as the difficulty in realizing the modularization and scale of DNA network construction, aggravating leakage and DNA sequence interference, and DNAzyme not participating in logical computing units, etc.

Active Publication Date: 2022-03-15
DALIAN UNIV
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AI Technical Summary

Problems solved by technology

[0004] In the above two methods, the assembly of DNAzyme sequences destroys the integrity of DNAzyme sequences, aggravates the leakage and interference between DNA sequences, and it is difficult to realize the modularization and scale of DNA network construction; the latter is only Applied to result detection, DNAzyme itself is a characteristic of DNA sequence, and DNAzyme is not involved in the functional structure of logical computing units

Method used

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  • A DNA Network Construction Method Based on Strand Displacement Regulation of E6 Ribozyme Function
  • A DNA Network Construction Method Based on Strand Displacement Regulation of E6 Ribozyme Function
  • A DNA Network Construction Method Based on Strand Displacement Regulation of E6 Ribozyme Function

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Embodiment 1

[0045] Embodiment 1 DNA YES logic gate

[0046] according to Figure 4 The construction method of the DNA YES logic gate in Figure 9 The analysis of the PAGE gel electrophoresis results of the YES logic gate is given. From the comparison of lane 1 and lane 2, the YES logic gate composed of sequences z1, t1, and r1 can be stably generated. Lane 3 shows the effect of E6 ribozyme on the RNA modification substrate Cutting effect of r1, when adding logic gate to trigger chain i1, YES logic gate gives correct output—chain o1 (lane 5). Figure 10 In order to correspond to the fluorescence detection result of the YES logic gate, compared with the fluorescence signal intensity when there is no input (Input=0), the fluorescence signal intensity of the YES logic gate is greatly enhanced (Output=1) when there is an input (Input=1) , indicating that the YES logic gate responds correctly to the input.

Embodiment 2

[0047] Embodiment 2 DNA OR logic gate

[0048] according to Figure 5 The construction method of DNA OR logic gate in Figure 11 It is the analysis of the PAGE gel electrophoresis results of the OR logic gate. By comparing the lanes 1 and 2, it can be known that the OR logic gate composed of the sequences z1, t2, and r1 can be stably generated. When trigger chains i2 (lane 5) and i3 (lane 5) and i3 (lane 6), the OR logic gate can output correctly, and when both input chains exist, the OR logic gate can also make a correct response (lane 7). Figure 12 It is the fluorescence detection result of the OR logic gate. Compared with the case of no input (Input=00), when the OR logic gate has any input (Input=10, 01, 11), the fluorescence signal intensity is greatly enhanced (Output=1), It shows that the OR logic gate can give correct calculation results for the four inputs of the OR operation.

Embodiment 3

[0049] Embodiment 3 DNA AND logic gate

[0050] according to Figure 6 The construction method of DNA AND logic gate in Figure 13 For the analysis of the PAGE gel electrophoresis results of AND logic gates, compare the electrophoresis bands of lane 1 and lane 2, and the AND logic gate composed of the sequence z2, t3, t4, r1 can be stably generated. When the AND gate has no input (lane 1), When there is only input i4 (lane 3) or only input i5 (lane 5), the E6 ribozyme z2 cannot cleave the substrate, that is, there is no output at this time. Enzyme z2 can cleave the substrate, and the output of the AND gate is 1 at this time. Figure 14 It is the fluorescence detection result of AND logic gate, when two inputs of AND logic gate all exist (Input=11), the intensity of fluorescence signal strengthens greatly (Output=1), and for other input situations (Input=00,01,10 ), and the intensity of the fluorescent signal weakens sharply (Output=0), which shows that the AND logic gate ca...

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Abstract

The invention relates to a DNA network construction method for regulating the function of E6 ribozyme based on strand displacement. Based on the hairpin-like secondary structure of the E6 ribozyme and the sequence of the catalytic core conservative domain, the method realizes the regulation of the function of the E6 ribozyme through strand displacement technology; the substrate binding arm of the E6 ribozyme is used to add an RNA-modified DNA substrate, Form a branch ring structure to construct a DNA logic computing unit; construct a DNA logic gate by transforming the DNA logic computing unit; finally connect the DNA logic gate to form a DNA network. The method does not destroy the sequence integrity of the E6 ribozyme, and the DNA logic computing unit has the characteristics of stable structure, customization, modularization, low leakage, and anti-interference, and can be widely used in biological computing and DNA nanostructures.

Description

technical field [0001] The invention belongs to the field of biological computing, and relates to a DNA chain replacement technology and a DNA ribozyme, in particular to a DNA network construction method based on strand replacement to regulate the function of an E6 ribozyme. Background technique [0002] With the development of molecular biology technology, biological computing has been widely concerned. In recent years, with the application of strand replacement technology, biological computing has successively realized basic computing functions such as biomolecular logic gates, biomolecular circuits, and DNA molecular machines. Biocomputing has gradually entered the stage of practical research from theoretical research. At present, most of the dynamic operations of biocomputing based on DNA molecules rely on the strand-exchange reaction of DNA sequences in the DNA network. In the reaction process, phenomena such as leakage and interference inevitably exist, making it diffi...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G16B15/00G16B5/00
CPCG16B15/00
Inventor 郑学东张强周昌军王宾
Owner DALIAN UNIV
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