Primerize-2D: automated primer design for RNA multidimensional chemical mapping.
Primerize-2D: automated primer design for RNA multidimensional chemical mapping.
复制标题
Primerize-2D：RNA 多维化学作图的自动化引物设计。
DOI：
10.1093/bioinformatics/btw814
复制
发表时间：
2017
期刊：
影响因子：
--
通讯作者：
Das,Rhiju
中科院分区：
文献类型：
--
作者：
Tian,Siqi;Das,Rhiju
综合性单突变体文库和靶向多突变体文库的快速RNA合成使新的多维化学方法能够解决RNA结构。DNA模板的PCR组装和体外转录允许以具有成本效益的方式合成和纯化数百种RNA突变体，其中跨构建体共享引物允许显著降低费用。然而，这些方案需要在许多96孔板上组织引物位置并指导移液，信息学和可视化工具可以防止代价高昂的错误的重要任务。我们在这里报告了一个在线工具，通过设计和有效组织引物来加速合成所需突变体的大型文库。底层程序和图形界面已经在我们的实验室中进行了实验测试，用于长度高达300个核苷酸的RNA结构域和包含多达960个变体的文库。除了免费提供的Primerize-2D服务器外，引物设计代码还可以作为独立的Python软件包提供，以用于更广泛的应用。可用性和实施http：//primerize2d.stanford.edu补充信息补充数据可在Bioinformatics online获得。
SummaryRapid RNA synthesis of comprehensive single mutant libraries and targeted multiple mutant libraries is enabling new multidimensional chemical approaches to solve RNA structures. PCR assembly of DNA templates andin vitrotranscription allow synthesis and purification of hundreds of RNA mutants in a cost-effective manner, with sharing of primers across constructs allowing significant reductions in expense. However, these protocols require organization of primer locations across numerous 96 well plates and guidance for pipetting, non-trivial tasks for which informatics and visualization tools can prevent costly errors. We report here an online tool to accelerate synthesis of large libraries of desired mutants through design and efficient organization of primers. The underlying program and graphical interface have been experimentally tested in our laboratory for RNA domains with lengths up to 300 nucleotides and libraries encompassing up to 960 variants. In addition to the freely available Primerize-2D server, the primer design code is available as a stand-alone Python package for broader applications.Availability and Implementationhttp://primerize2d.stanford.eduSupplementary informationSupplementary data are available atBioinformaticsonline.