title: AmiRNA Designer - new method of artificial miRNA design.
abstract: MicroRNAs (miRNAs) are small non-coding RNAs that have been found in most of the eukaryotic organisms. They are involved in the regulation of gene expression at the post-transcriptional level in a sequence specific manner. MiRNAs are produced from their precursors by Dicer-dependent small RNA biogenesis pathway. Involvement of miRNAs in a wide range of biological processes makes them excellent candidates for studying gene function or for therapeutic applications. For this purpose, different RNA-based gene silencing techniques have been developed. Artificially transformed miRNAs (amiRNAs) targeting one or several genes of interest represent one of such techniques being a potential tool in functional genomics. Here, we present a new approach to amiRNA*design, implemented as AmiRNA Designer software. Our method is based on the thermodynamic analysis of the native miRNA/miRNA* and miRNA/target duplexes. In contrast to the available automated tools, our program allows the user to perform analysis of natural miRNAs for the organism of interest and to create customized constraints for the design stage. It also provides filtering of the amiRNA candidates for the potential off-targets. AmiRNA Designer is freely available at http://www.cs.put.poznan.pl/arybarczyk/AmiRNA/.
authors.affiliation: Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland.
authors.forename: Agnieszka
authors.initials: A
authors.lastname: Mickiewicz
authors.affiliation: Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland and Institute of Computing Science, Poznan University of Technology, Poznań, Poland.
authors.forename: Agnieszka
authors.initials: A
authors.lastname: Rybarczyk
authors.affiliation: Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland.
authors.forename: Joanna
authors.initials: J
authors.lastname: Sarzynska
authors.affiliation: Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland and Institute of Computing Science, Poznan University of Technology, Poznań, Poland.
authors.forename: Marek
authors.initials: M
authors.lastname: Figlerowicz
authors.affiliation: Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland and Institute of Computing Science, Poznan University of Technology, Poznań, Poland.
authors.forename: Jacek
authors.initials: J
authors.lastname: Blazewicz
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D001331:Automation; D035683:MicroRNAs / Q000138:chemical synthesis* / Q000737:chemistry / Q000235:genetics; D018749:RNA, Plant / Q000138:chemical synthesis / Q000737:chemistry / Q000235:genetics; D013816:Thermodynamics
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant