A high-performance computing platform-based computer-aided screening method for nucleic acid aptamers and nucleic acid aptamers

Abstract

The invention provides a nucleic acid adapter computer-aided screening method based on a high-performance calculating platform, wherein the method relates to the field of molecular biology detecting technology. According to a matching principle, whether a protein structure which matches a target protein exists in a database system which is integrated in a screening platform is determined through searching; if yes, the protein structure is used as an acceptor template; and otherwise, homologous construction is performed. A primary selected nucleic acid adaptor is obtained through modular dynamics simulation and molecular docking screening as a nucleic acid adaptor candidate. The method and the nucleic acid adapter have advantages of high efficiency, high speed and high accuracy. The screening method can be combined with wet-method experiments, thereby reducing the number of the wet-method experiments, saving experiment cost and improving screening success rate. Through computer-aided simulation analysis, information such as chemical reaction mechanism between the protein and nucleic acid molecule in an adaption process is obtained. Furthermore the data are displayed on a terminal. Furthermore a data support is supplied at an aspect of disclosing a possible interaction mechanism between a corresponding biomaterial and the nucleic acid molecule. Therefore the method and the nucleic acid adapter have an important researching meaning and high use value.

Description

Technical field[0001]The present invention relates to the field of molecular biological detection, and more particularly to a nucleic acid adapter computer assisted screening method based on a high performance computing platform.Background technique[0002]Computational biology is a vibrant emerging cross-discipline, which is constantly playing an important role in the current biology research, and is an important tool for the study of biological mechanism. Computational biology can accomplish a large number of biological data and complex calculation processes, and is the current intersection of life disciplines and non-life disciplines, which has an efficient and convenient feature. Computer-aided design, comparative genomic analysis, biological system model, cellular signaling, and genetically regulated network research, expert database, biological software package, etc.[0003]Computational protein nucleic acid docking techniques in biology are effective methods for predicting the st...

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Problems solved by technology

[0006] (1) Aptamers from Cell-Based Selection for Bioanalytical Applications, Chemical Reviews, 2013, 113, 2842-2862, this prior art introduces a current screening method for cellular nucleic acid aptamers, generally requiring about 20 rounds of screening , in order to obtain high-affinity nucleic acid aptamers, the number of realizations is relatively large, and the screening process is complicated and time-consuming

[0007] (2) The announcement number is: CN103911379, the patent name is: nucleic acid aptamers and their derivatives, screening methods and applications, using the characteristics of single-walled carbon nanotubes that can adsorb single-stranded DNA very well, the single-walled carbon nanotubes Introduced into the screening process to reduce non-specific adsorption and effectively remove bound single-stranded DNA. Although the number of times of this method has been reduced correspondingly, the number of times is still relatively large, and it is difficult to automate

[0008] It can be seen that the traditional nucleic acid aptamer screening method is that the nucleic acid aptamers are screened by the systemic evolution of ligands by exponential enrichment (SELEX) technology, and the pre-enriched nucleic acid library needs to be Sequencing, and then selecting nucleic acid aptamer sequences with high affinity and good selectivity from a large number of sequencing results, this process has the problems of long time-consuming, low efficiency, high cost, and difficulty in automation

That is, the method has a long period, a large amount of labor, and a high cost. In addition, the excessive number of trials and the trial period will cause a mismatch between ssDNA and drDNA to convert each other. In each convergence process, the target sequence is not obtained. Amplification, resulting in loss of the target sequence

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