G-quadruplex nucleic acid aptamer tertiary structure prediction method of targeted biotoxin
A nucleic acid aptamer, biotoxin technology, applied in biological systems, bioinformatics, informatics, etc., can solve the problems of complexity, difficult computational simulation, slow folding of G-quadruplexes, etc., and achieve the effect of accurate prediction
Active Publication Date: 2020-01-21
FUDAN UNIV
View PDF6 Cites 3 Cited by
- Summary
- Abstract
- Description
- Claims
- Application Information
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
Method used
the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
View moreImage
Smart Image Click on the blue labels to locate them in the text.
Smart ImageViewing Examples
Examples
Experimental program
Comparison scheme
Effect test
Embodiment Construction
[0030] The method of the present invention is specifically applied to the process of G-quadruplex nucleic acid aptamer GO18-T-d targeting gonyellin:
[0031] Step 1: G-quadruplex secondary structure prediction
[0032] The first step of the prediction procedure is the G-quadruplex secondary structure prediction of the GO18-T-d sequence. After obtaining the GO18-T-d nucleotide sequence (5'-AACCTTTGGTCGGGCAAGGTAGGTT-3' (SEQ. ID. NO1)), its secondary structure was predicted using the QGRS Mapper website. In QGRS Mapper, all possible G-quadruplet secondary structures are ranked according to their score: the higher the score, the more likely it exists as this structure. The results showed that the G value of GO18-T-d was as high as 20, indicating a high possibility of forming a G-quadruplex structure.
[0033] Step 2: G-quadruplex tertiary topology prediction
[0034] In the second step, the G-quadruplex tertiary topology is predicted for the secondary structure with the highest...
the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
Login to View More PUM
Login to View More 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...
Claims
the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
Login to View More Application Information
Patent Timeline
Login to View More Patent Type & Authority Applications(China)
IPC IPC(8): G16B5/00G16B50/00
CPCG16B5/00G16B50/00
Inventor 黄强刘建平章琪李干宋梦华
Owner FUDAN UNIV