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现代化工  2018, Vol. 38 Issue (11): 216-220    DOI: 10.16606/j.cnki.issn0253-4320.2018.11.047
  信息技术应用 本期目录 | 过刊浏览 | 高级检索 |
计算机模拟在优化核酸适体筛选分析流程中的应用研究
王明华1, 李杜娟2
1. 忻州师范学院生物系, 山西 忻州 034000;
2. 杭州电子科技大学生命信息与仪器工程学院, 浙江 杭州 310018
Application of computer simulation in optimization of nucleic acid aptamer screening and analysis
WANG Ming-Hua1, LI Du-Juan2
1. Biology Department, Xinzhou Teachers University, Xinzhou 034000, China;
2. College of Life Information Science and Instrument Engineering, Hangzhou Dianzi University, Hangzhou 310018, China
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摘要 通过分析列举成功筛选应用实例及研究新趋势,对计算机模拟辅助虚拟筛选核酸适体方法的适用性、程序性、必要性进行综述和分析,为计算机虚拟筛选技术推动核酸适体的开发和应用提供新的思路。
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王明华
李杜娟
关键词:  适体  分子模拟  结构预测  虚拟筛选    
Abstract: This paper reviews and analyzes the applicability,procedure and necessity of the method for virtual screening nucleic acid aptamer assisted by computer simulation,based on listing the successful application examples in screening and studying new trends.It aims to provide a new idea for computer virtual screening technology to promote the development and application of nucleic acid aptamers.
Key words:  aptamer    molecular simulation    structure prediction    virtual screening
收稿日期:  2018-04-12      修回日期:  2018-09-05          
O6-04  
  O629.7  
  Q811.4  
基金资助: 国家自然科学基金项目(31201367);浙江省自然科学基金项目(LY15H200003);忻州师范学院博士启动基金(2015)
通讯作者:  李杜娟(1983-),女,博士,副研究员,研究方向为生物传感器,通讯联系人,dujuanli@hdu.edu.cn。    E-mail:  dujuanli@hdu.edu.cn
作者简介:  王明华(1982-),女,博士,副教授,研究方向为生物大分子结构与功能,wmh820312@126.com
引用本文:    
王明华, 李杜娟. 计算机模拟在优化核酸适体筛选分析流程中的应用研究[J]. 现代化工, 2018, 38(11): 216-220.
WANG Ming-Hua, LI Du-Juan. Application of computer simulation in optimization of nucleic acid aptamer screening and analysis. Modern Chemical Industry, 2018, 38(11): 216-220.
链接本文:  
http://www.xdhg.com.cn/CN/10.16606/j.cnki.issn0253-4320.2018.11.047  或          http://www.xdhg.com.cn/CN/Y2018/V38/I11/216
[1] Bock L C,Griffin L C,Latham J A,et al.Selection of single-stranded DNA molecules that bind and inhibit human thrombin[J].Nature,1992,355(6360):564-566.
[2] Draper D E.Themes in RNA-protein recognition[J].Journal of Molecular Biology,1999,293(2):255-270.
[3] Brooks B R,Ma Jr,Nilsson L,et al.CHARMM:The biomolecular simulation program[J].Journal of Computational Chemistry,2009,30(10):1545-1614.
[4] Szczesniak M W,Makalowska I.lncRNA-RNA interactions across the human transcriptome[J].PloS One,2016,11:e0150353.
[5] Fiannaca A,Rosa M L,Paglia L L,et al.nRC:Non-coding RNA classifier based on structural features[J].Biodata Mining,2017,10(8):e27.
[6] Collie G W,Parkinson G N.The application of DNA and RNA G-quadruplexes to therapeutic medicines[J].Chemical Society Reviews,2012,40(12):5867-5892.
[7] Nawrocki E P,Burge S W,Bateman A,et al.Rfam 12.0:Updates to the RNA families database[J].Nucleic Acids Research,2015,43(D1):D130-D137.
[8] Zuker M.Mfold web server for nucleic acid folding and hybridization prediction[J].Nucleic Acids Research,2003,31(13):3406-3415.
[9] Reuter J S,Mathews D H.RNA structure:Software for RNA secondary structure prediction and analysis[J].BMC Bioinformatics,2010,11(1):e129.
[10] Miladi M,Junge A,Costa F,et al.RNAscClust:Clustering RNA sequences using structure conservation and graph based motifs[J].Bioinformatics,2017,33(14):2089-2096.
[11] Shi J,Li X,Dong M,et al.JNSViewer-A java script-based nucleotide sequence viewer for DNA/RNA secondary structures[J].Plos One,2017,12(6):e0179040.
[12] Biesiada M,Purzycka K J,Szachniuk M,et al.Automated RNA 3D structure prediction with RNA composer[J].Methods in Molecular Biology,2016,1490(6):199-215.
[13] Das R,Baker D.Automated de novo prediction of native-like RNA tertiary structures[J].Proceedings of the National Academy of Sciences of the United States of America,2007,104:14664-14669.
[14] Dijk M V,Bonvin A M J J.3D-DART:A DNA structure modelling server[J].Nucleic Acids Research,2009,37(7):W235-W239.
[15] Snodin B E,Romano F,Rovigatti L,et al.Direct simulation of the self-assembly of a small DNA origami[J].Acs Nano,2016,10(2):1724-1737.
[16] Jeddi I,Saiz L.Three-dimensional modeling of single stranded DNA hairpins for aptamer-based biosensors[J].Scientific Reports,2017,7(4):e1178.
[17] Alexandra S P,Ruth N,Wolfson H J.RsiteDB:A database of protein binding pockets that interact with RNA nucleotide bases[J].Nucleic Acids Research,2009,37(1):D369-D373.
[18] Tuyshinjargal N,Lee W,Park B,et al.PRIdictor:Protein-RNA interaction predictor[J].Biosystems,2016,139(1):17-22.
[19] Pierce B G,Wiehe K,Hwang H,et al.ZDOCK Server:Interactive docking prediction of protein-protein complexes and symmetric multimers[J].Bioinformatics,2014,30(12):1771-1773.
[20] Gray J J,Moughon S,Wang C,et al.Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations[J].Journal of Molecular Biology,2003,331(1):281-299.
[21] Tuszynska I,Magnus M,Jonak K,et al.NPDock:A web server for protein-nucleic acid docking[J].Nucleic Acids Research,2015,43(W1):W425-W430.
[22] Shcherbinin D S,Gnedenko O V,Khmeleva S A,et al.Computer-aided design of aptamers for cytochrome p450[J].Journal of Structural Biology,2015,191(2):112-119.
[23] Heiat M,Najafi A,Ranjbar R,et al.Computational approach to analyze isolated ssDNA aptamers against angiotensin Ⅱ[J].Journal of Biotechnology,2016,230:34-39.
[24] Chushak Y,Stone M O.In silico selection of RNA aptamers[J].Nucleic Acids Research,2009,37(12):e87.
[25] Savory N,Lednor D,Tsukakoshi K,et al.In silico maturation of binding-specificity of DNA aptamers against proteus mirabilis[J].Biotechnology and Bioengineering,2013,110(10):2573-2580.
[26] Savory N,Nzakizwanayo J,Abe K,et al.Selection of DNA aptamers against uropathogenic Escherichia coli NSM59 by quantitative PCR controlled Cell-SELEX[J].Journal of Microbiological Methods,2014,104(9):94-100.
[27] Yokoyama T,Tsukakoshi K,Yoshida W,et al.Development of HGF-binding aptamers with the combination of G4 promoter-derived aptamer selection and in silico maturation[J].Biotechnology and Bioengineering,2017,114(10):2196-2203.
[28] Fukaya T,Abe K,Savory N,et al.Improvement of the VEGF binding ability of DNA aptamers through in silico maturation and multimerization strategy[J].Journal of Biotechnology,2015,212(6863):99-105.
[29] Zhou Q,Xia X,Luo Z.Searching the sequence space for potent aptamers using SELEX in silico[J].Journal of Chemical Theory and Computation,2015,11(12):5939-5946.
[30] Ahirwar R,Nahar S,Aggarwal S,et al.In silico selection of an aptamer to estrogen receptor alpha using computational docking employing[J].Scientific reports,2016,6(2):e21285.
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