title: siRNA selection criteria--statistical analyses of applicability and significance.
abstract: RNA interference is a powerful tool for gene silencing, which is mediated by introducing siRNA. In the present study, statistical analyses of published siRNA selection criteria, the interpretation of some criteria and systematic searching for new criteria have been carried out for CGB siRNA and siRecords databases. The results of the analyses are as follows: (i) Our study supports the two-state model of the RNA-induced silencing complex (RISC). (ii) Stable 5'-S ends of a siRNA sequence, higher stability of the whole siRNA, and low breaking energy of siRNA duplex occurs in effective siRNA sequences. Also low internal stability of the 5'-AS terminus is preferred. (iii) Secondary structure can be successfully used as an RNAi selection criterion. (iv) Several published sequence criteria have been confirmed and also new criteria have been developed. (v) Also a Target Patterns criterion, which is comparable or better than the best known criteria, has been created.
authors.affiliation: Bioinformatics group, ANF DATA (subsidiary of Siemens), Herspická 5, 639 00 Brno, Czech Republic.
authors.forename: Ivan
authors.initials: I
authors.lastname: Bradác
authors.forename: Radka
authors.initials: R
authors.lastname: Svobodová Vareková
authors.forename: Michael
authors.initials: M
authors.lastname: Wacenovsky
authors.forename: Michal
authors.initials: M
authors.lastname: Skrdla
authors.forename: Martin
authors.initials: M
authors.lastname: Plchút
authors.forename: Martin
authors.initials: M
authors.lastname: Polcík
mesh_terms: D001483:Base Sequence; D003627:Data Interpretation, Statistical; D020868:Gene Silencing; D008957:Models, Genetic; D015233:Models, Statistical; D008969:Molecular Sequence Data; D034741:RNA, Small Interfering / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D034741:RNA, Small Interfering