Structure-based nucleic acid aptamer optimization design method
A nucleic acid aptamer and optimized design technology, which is used in the analysis of two-dimensional or three-dimensional molecular structures, genomics, instruments, etc., can solve problems such as difficult mass application, and achieve the effect of improving affinity
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[0027] The specific process of the method of the present invention will be further described below by taking the optimal design method of the G-quadruplex nucleic acid aptamer GO18-T-d targeting GTX1 / 4 (gonyautoxin 1 / 4) as an example.
[0028] Step 1: Perform a spontaneous binding molecular dynamics simulation
[0029] The first step is an unbiased spontaneous binding simulation with the goal of obtaining a stable and plausible 3D structure of the GO18-T-d:GTX1 / 4 complex. The sequence of the nucleic acid aptamer GO18-T-d and the structure of the toxin small molecule GTX1 / 4 are as follows figure 2shown. The structure of GO18-T-d was generated by the AutoPSF plugin in 3D-Nus(13) and VMD(14), and screened by temperature-dependent molecular dynamics simulations. The GAFF parameters of the toxin molecule GTX1 / 4 were generated using the Antechamber software package that comes with AmberTools. After obtaining the force field parameters of the small molecule, in order to avoid the...
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