title: What parameters to consider and which software tools to use for target selection and molecular design of small interfering RNAs.
abstract: The design of small gene silencing RNAs with a high probability of being efficient still has some elements of an art, especially when the lowest concentration of small molecules needs to be utilized. The design of highly target-specific small interfering RNAs or short hairpin RNAs is even a greater challenging task. Some logical schemes and software tools that can be used for simplifying both tasks are presented here. In addition, sequence motifs and sequence composition biases of small interfering RNAs that have to be avoided because of specificity concerns are also detailed.
authors.affiliation: Department of Human Genetics, University of Utah, Salt Lake City, UT, USA. olga.matveeva@gmail.com
authors.forename: Olga
authors.initials: O
authors.lastname: Matveeva
mesh_terms: D000465:Algorithms; D020868:Gene Silencing; D005818:Genetic Engineering / Q000379:methods*; D006801:Humans; D020871:RNA Stability; D012330:RNA, Double-Stranded / Q000737:chemistry / Q000235:genetics; D034741:RNA, Small Interfering / Q000737:chemistry / Q000235:genetics*; D012984:Software
chemical_list: D012330:RNA, Double-Stranded; D034741:RNA, Small Interfering