Tertiary structure prediction method of g-quadruplex nucleic acid aptamer targeting biotoxin

Abstract

The invention belongs to the technical field of nucleotide tertiary structure prediction, and particularly relates to a G-quadruplex nucleic acid aptamer tertiary structure prediction method of targeted biotoxin. The method comprises the following steps: predicting a G-quadruplex secondary structure; predicting a G-quadruplex tertiary topological configuration; carrying out nucleic acid aptamer tail end complementation and structure optimization; carrying out temperature-dependent molecular dynamics simulation (comprising two processes: constant-temperature molecular dynamics simulation and heating molecular dynamics simulation); and obtaining a most stable nucleic acid tertiary structure model by adopting an RMSD analysis method. The method disclosed by the invention is already used for predicting a tertiary structure of a specific nucleic acid aptamer sequence GO18-T-d of the targeted gonyautoxin; the sequence is a known G-quadruplex aptamer sequence obtained by screening through anexponential enrichment ligand evolution technology, the G-quadruplex configuration is detected to be a parallel G-quadruplex configuration through a circular dichroism experiment, a prediction resultis completely matched with a detection result of the circular dichroism experiment, and it is proved that the prediction method has good accuracy.

Description

technical field [0001] The invention belongs to the technical field of nucleotide tertiary structure prediction, and in particular relates to a method for tertiary structure prediction of a G-quadruplex nucleic acid aptamer targeting biological toxins. Background technique [0002] In recent years, the G-quadruplex structure of nucleic acid has attracted more and more attention from researchers, because they play an important role in regulating the metabolic activities of various organisms [1,2] . On the other hand, the G-quadruplex has good stability and specificity, and can efficiently and specifically recognize small molecules, organelles and even whole cells, making it have great potential in the field of detection [3] . In the process of obtaining G-quadruplex nucleic acid aptamers targeting target molecules, people often use SELEX technology (systematicevolution of ligands by exponential enrichment, SELEX) to obtain G-quadruplex aptamer sequences. However, traditiona...

AI Technical Summary

Problems solved by technology

However, G-quadruplex folding is a slow and extremely complex process, and it is very difficult to accurately predict this process from the perspective of computational simulations

For these nine types of topologies, there is currently no credible structure prediction method that accurately predicts the native tertiary structure of the G-quadruplex

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