Tian Siqi, Yesselman Joseph D, Cordero Pablo, Das Rhiju
Departments of Biochemistry, Stanford University, Stanford CA 94305, USA.
Program in Biomedical Informatics, Stanford University, Stanford CA 94305, USA.
Nucleic Acids Res. 2015 Jul 1;43(W1):W522-6. doi: 10.1093/nar/gkv538. Epub 2015 May 20.
Customized RNA synthesis is in demand for biological and biotechnological research. While chemical synthesis and gel or chromatographic purification of RNA is costly and difficult for sequences longer than tens of nucleotides, a pipeline of primer assembly of DNA templates, in vitro transcription by T7 RNA polymerase and kit-based purification provides a cost-effective and fast alternative for preparing RNA molecules. Nevertheless, designing template primers that optimize cost and avoid mispriming during polymerase chain reaction currently requires expert inspection, downloading specialized software or both. Online servers are currently not available or maintained for the task. We report here a server named Primerize that makes available an efficient algorithm for primer design developed and experimentally tested in our laboratory for RNA domains with lengths up to 300 nucleotides. Free access: http://primerize.stanford.edu.
定制化RNA合成在生物学和生物技术研究中很有需求。虽然RNA的化学合成以及凝胶或色谱纯化对于长度超过数十个核苷酸的序列来说成本高昂且困难，但DNA模板的引物组装、T7 RNA聚合酶的体外转录以及基于试剂盒的纯化流程为制备RNA分子提供了一种经济高效且快速的替代方法。然而，设计能够优化成本并避免聚合酶链反应期间错配的模板引物目前需要专家检查、下载专门软件或两者兼备。目前尚无用于此任务的在线服务器或维护。我们在此报告一个名为Primerize的服务器，它提供了一种高效的引物设计算法，该算法是在我们实验室针对长度达300个核苷酸的RNA结构域开发并经过实验测试的。免费访问：http://primerize.stanford.edu。
