title: Primerize: automated primer assembly for transcribing non-coding RNA domains.
abstract: 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.
authors.affiliation: Departments of Biochemistry, Stanford University, Stanford CA 94305, USA.
authors.forename: Siqi
authors.initials: S
authors.lastname: Tian
authors.affiliation: Departments of Biochemistry, Stanford University, Stanford CA 94305, USA.
authors.forename: Joseph D
authors.initials: JD
authors.lastname: Yesselman
authors.affiliation: Program in Biomedical Informatics, Stanford University, Stanford CA 94305, USA.
authors.forename: Pablo
authors.initials: P
authors.lastname: Cordero
authors.affiliation: Departments of Biochemistry, Stanford University, Stanford CA 94305, USA Program in Biomedical Informatics, Stanford University, Stanford CA 94305, USA Department of Physics, Stanford University, Stanford CA 94305, USA rhiju@stanford.edu.
authors.forename: Rhiju
authors.initials: R
authors.lastname: Das
mesh_terms: D000465:Algorithms; D017931:DNA Primers / Q000737:chemistry*; D020407:Internet; D009690:Nucleic Acid Conformation; D016133:Polymerase Chain Reaction; D022661:RNA, Untranslated / Q000096:biosynthesis*; D017422:Sequence Analysis, DNA; D012984:Software; D013698:Templates, Genetic; D014158:Transcription, Genetic
chemical_list: D017931:DNA Primers; D022661:RNA, Untranslated