title: siPools: highly complex but accurately defined siRNA pools eliminate off-target effects.
abstract: Short interfering RNAs (siRNAs) are widely used as tool for gene inactivation in basic research and therapeutic applications. One of the major shortcomings of siRNA experiments are sequence-specific off-target effects. Such effects are largely unpredictable because siRNAs can affect partially complementary sequences and function like microRNAs (miRNAs), which inhibit gene expression on mRNA stability or translational levels. Here we demonstrate that novel, enzymatically generated siRNA pools-referred to as siPools-containing up to 60 accurately defined siRNAs eliminate off-target effects. This is achieved by the low concentration of each individual siRNA diluting sequence-specific off-target effects below detection limits. In fact, whole transcriptome analyses reveal that single siRNA transfections can severely affect global gene expression. However, when complex siRNA pools are transfected, almost no transcriptome alterations are observed. Taken together, we present enzymatically produced complex but accurately defined siRNA pools with potent on-target silencing but without detectable off-target effects.
authors.affiliation: Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany Intana Biosciences GmbH, Lochhamerstrasse 29A, 82152 Martinsried/Planegg, Germany siTools Biotech GmbH, Lochhamerstrasse 29A, 82152 Martinsried/Planegg, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Hannus
authors.affiliation: Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany siTools Biotech GmbH, Lochhamerstrasse 29A, 82152 Martinsried/Planegg, Germany.
authors.forename: Michaela
authors.initials: M
authors.lastname: Beitzinger
authors.affiliation: Department of Statistical Bioinformatics, Institute for Functional Genomics, University of Regensburg, Josef-Engert-Straße 9, 93053 Regensburg, Germany.
authors.forename: Julia C
authors.initials: JC
authors.lastname: Engelmann
authors.affiliation: Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany.
authors.forename: Marie-Theresa
authors.initials: MT
authors.lastname: Weickert
authors.affiliation: Department of Statistical Bioinformatics, Institute for Functional Genomics, University of Regensburg, Josef-Engert-Straße 9, 93053 Regensburg, Germany.
authors.forename: Rainer
authors.initials: R
authors.lastname: Spang
authors.affiliation: Intana Biosciences GmbH, Lochhamerstrasse 29A, 82152 Martinsried/Planegg, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Hannus
authors.affiliation: Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany gunter.meister@vkl.uni-regensburg.de.
authors.forename: Gunter
authors.initials: G
authors.lastname: Meister
mesh_terms: D006367:HeLa Cells; D006801:Humans; D007372:Interferons / Q000494:pharmacology; D005810:Multigene Family; D034622:RNA Interference; D012333:RNA, Messenger / Q000378:metabolism; D034741:RNA, Small Interfering / Q000096:biosynthesis / Q000378:metabolism*
chemical_list: D012333:RNA, Messenger; D034741:RNA, Small Interfering; D007372:Interferons