AmiRNA Designer - new method of artificial miRNA design.

Agnieszka Mickiewicz; Agnieszka Rybarczyk; Joanna Sarzynska; Marek Figlerowicz; Jacek Blazewicz

doi:10.18388/abp.2015_989

Agnieszka Mickiewicz Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland.;
Agnieszka Rybarczyk Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland and Institute of Computing Science, Poznan University of Technology, Poznań, Poland.;
Joanna Sarzynska Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland.;
Marek Figlerowicz Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland and Institute of Computing Science, Poznan University of Technology, Poznań, Poland.;
Jacek Blazewicz Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland and Institute of Computing Science, Poznan University of Technology, Poznań, Poland.;

DOI: https://doi.org/10.18388/abp.2015_989

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/.