Aptamer design method based on single-nucleotide molecular docking

A nucleic acid aptamer, molecular docking technology, applied in biochemical equipment and methods, genetic engineering, microbial assay/inspection, etc. question

Active Publication Date: 2021-01-12
FUDAN UNIV
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Problems solved by technology

But the traditional SELEX technology often has the problem of low efficiency and hit rate(5)
This is because the oligonucleotide library cannot synthesize all possible olig

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  • Aptamer design method based on single-nucleotide molecular docking
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  • Aptamer design method based on single-nucleotide molecular docking

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Embodiment Construction

[0034] The specific process of the method of the present invention will be further described below by taking the computational design method of the nucleic acid aptamer OA-D1 targeting OA (Okadaic acid) as an example.

[0035] Step 1: Perform hydration docking of single nucleotides to obtain the position of single nucleotides bound to the surface of small toxin molecules;

[0036] The first step aims to obtain the positions of mononucleotides bound on the OA surface. The molecular docking method can quickly find the main binding site of OA and the binding position of each nucleotide (A, C, G, T) on its surface. In the first docking, the receptor molecule is the toxin small molecule OA, its structure comes from the PDB database (ID: 2I4E), and the ligand molecule is each nucleotide; in the second molecular docking, the receptor molecule is the toxin small molecule OA And the nucleotides retained after docking, the ligand molecule is still each nucleotide. The software used fo...

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Abstract

The invention belongs to the technical field of aptamer design, and particularly relates to an aptamer design method based on single-nucleotide molecular docking. Starting from an experimental structure of a target small molecule, positions of nucleotides combined around the target small molecule are obtained through hydration docking; then, the discrete nucleotides are assembled into a complete aptamer; and finally, the binding capacity of the designed aptamer and the target small molecule is detected by adopting an MST experiment. The aptamer design method in the invention has been used in the design of aptamers of toxin small molecule okadaic acid (OA); the toxin is a widely distributed marine biological toxin, and can cause diarrhea type shellfish poisoning, so that the detection of OAin marine products is of great significance to food safety; an aptamer OA-D1 targeting OA is obtained by design through a calculation method; the MST experiment verifies that the equilibrium dissociation constant of the aptamer and OA is 75.6 nM; and therefore, the calculation design method is reasonable and effective.

Description

technical field [0001] The invention belongs to the technical field of nucleic acid aptamer design, and in particular relates to a nucleic acid aptamer design method. Background technique [0002] Aptamers are ribonucleic acid (RNA) or single-stranded deoxyribonucleic acid (ssDNA) with high affinity to specific targets, which can be folded to form stable secondary or tertiary structures through hydrogen bond interactions between bases in the chain ( 2,3). Nucleic acid aptamers are generally composed of dozens of nucleotides, with small molecular weight, stable properties, easy preparation and modification, and can bind to targets such as ions, small molecules, proteins, cells and microorganisms. Nucleic acid aptamers that bind to small molecule targets can specifically recognize and distinguish extremely small differences between small molecules, and are usually used as recognition molecules for chemical and microbial sensors, and are widely used in food and environmental m...

Claims

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Application Information

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IPC IPC(8): C12Q1/6811C12N15/115
CPCC12N15/115C12N2310/16C12Q1/6811C12Q2525/205C12Q2525/301C12Q2563/107
Inventor 黄强宋梦华刘建平颜志超李园园
Owner FUDAN UNIV
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