AAscan, PCRdesign and MutantChecker: a suite of programs for primer design and sequence analysis for high-throughput scanning mutagenesis.
AAscan, PCRdesign and MutantChecker: a suite of programs for primer design and sequence analysis for high-throughput scanning mutagenesis.
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DOI：
10.1371/journal.pone.0078878
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Veprintsev DB
中科院分区：
文献类型：
--
作者：
Sun D;Ostermaier MK;Heydenreich FM;Mayer D;Jaussi R;Standfuss J;Veprintsev DB
扫描诱变是一种强大的蛋白质工程技术，用于研究蛋白质结构与功能的关系，定位结合位点，设计更稳定的蛋白质或改变性质的蛋白质。在应用该技术中遇到的耗时任务之一是设计用于定点诱变的引物。在这里，我们提出了一个开源的多平台软件AAscan开发设计引物的任务，根据一组经验规则，如解链温度，总长度，重叠区的长度，并在3'端的GC钳的存在下，任何所需的取代。我们还描述了用于分析大量测序结果中所需突变的存在的其他软件工具，以及设计用于连接非依赖性克隆的引物的相关软件。我们利用AAscan软件设计引物，获得了700多个突变体，成功率超过80%。我们希望，我们的软件的开放源码性质和用于其开发的免费软件工具的现成可用性将促进其适应和进一步发展。该软件在GPL v3许可下分发，可在http://www.psi.ch/lbr/aascan上获得。
Scanning mutagenesis is a powerful protein engineering technique used to study protein structure-function relationship, map binding sites and design more stable proteins or proteins with altered properties. One of the time-consuming tasks encountered in application of this technique is the design of primers for site-directed mutagenesis. Here we present an open-source multi-platform software AAscan developed to design primers for this task according to a set of empirical rules such as melting temperature, overall length, length of overlap regions, and presence of GC clamps at the 3’ end, for any desired substitution. We also describe additional software tools which are used to analyse a large number of sequencing results for the presence of desired mutations, as well as related software to design primers for ligation independent cloning. We have used AAscan software to design primers to make over 700 mutants, with a success rate of over 80%. We hope that the open-source nature of our software and ready availability of freeware tools used for its development will facilitate its adaptation and further development. The software is distributed under GPLv3 licence and is available at http://www.psi.ch/lbr/aascan.
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