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

Active Publication Date: 2020-02-07
FUDAN UNIV
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Problems solved by technology

However, nucleic acid aptamers have strong flexibility, an

Method used

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  • Structure-based nucleic acid aptamer optimization design method
  • Structure-based nucleic acid aptamer optimization design method
  • Structure-based nucleic acid aptamer optimization design method

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Embodiment Construction

[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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Abstract

The invention belongs to the technical field of nucleic acid aptamer design and particularly relates to a structure-based nucleic acid aptamer optimization design method. The method is characterized in that starting from a 3D structure of a nucleic acid aptamer screened by the SELEX technology, a 3D structure of a compound formed by combining small molecules with the nucleic acid aptamer is obtained through spontaneous combination simulation; the structure of the compound and key combination sites are analyzed, and optimal design of the high-affinity nucleic acid aptamer is guided by utilizingthe obtained information; a design scheme is evaluated by adopting a performance diagram of nucleic acid aptamer surface combination energy. The method is advantaged in that the method is applied tooptimization design of the nucleic acid aptamer GO18-T-d of specifically combined toxin GTX1/4; the nucleic acid aptamer is obtained by screening through the SELEX technology, and affinity is 75.63 nM; a truncated nucleic acid aptamer (GO18-T-d_S) of GO18-T-d is obtained through optimization, and that the affinity of the nucleic acid aptamer is improved by 20 times is verified through an MST experiment, and the optimization 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 optimal 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 ( 1,2). 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 tiny differences between small molecules, and are usually used as recognition molecules for chemical and microbial sensors, and are widely used in food and environmental moni...

Claims

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Application Information

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IPC IPC(8): G16B5/20G16B15/10G16B20/30
CPCG16B5/20G16B15/10G16B20/30
Inventor 黄强宋梦华刘建平章琪李干
Owner FUDAN UNIV
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