A nucleic acid aptamer design method based on single nucleotide molecular docking

Abstract

The invention belongs to the technical field of nucleic acid aptamer design, in particular to a nucleic acid aptamer design method based on single nucleotide molecule docking. The present invention starts from the experimental structure of the target small molecule, obtains the nucleotide positions bound around the target small molecule through hydration docking; then assembles the discrete nucleotides into a complete nucleic acid aptamer; finally uses the MST experiment to detect the designed The binding ability of nucleic acid aptamers to target small molecules. The present invention has been used in the nucleic acid aptamer design of toxin small molecule okadaic acid (OA); Food safety is of great significance. The nucleic acid aptamer OA‑D1 targeting OA was designed by computational method, and the equilibrium dissociation constant between the nucleic acid aptamer and OA was verified to be 75.6 nM by MST experiments, which indicated that the computational design method was 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...

AI Technical Summary

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 oligonucleotide chains, and there are differences in the synthesis speed of different types of oligonucleotide chains, which will affect the screening of nucleic acid aptamers

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