title: Comparison of test systems for RNAinterference.
abstract: RNAinterference (RNAi) has developed within a short time from an area of basic research occupied by a few experts to a widely used technical tool for reverse genetics, which is expected to have a broad utility not only in research, but also in medical and diagnostic applications. Despite its widespread use, the application of RNAi is often hampered because a difference of only a few nucleotides in the sequence of the target RNA can change the efficiency of a small interfering RNA (siRNA) from high to zero, and publicly available design tools for siRNAs are not yet perfect. We therefore developed and compared RNAi test systems based on different promoters, reporters, and target sequences. Here, we show that fluorescence-based test systems have obvious disadvantages compared to luciferase-based test systems and that some combinations of promoter, reporter, and target sequences, although currently in use, are not well suited for testing RNAi effects.
authors.affiliation: DFG Center of Molecular Physiology of the Brain at the Department of Neurology, University of Göttingen, Germany.
authors.forename: Ibrahim
authors.initials: I
authors.lastname: Malik
authors.forename: Manuel
authors.initials: M
authors.lastname: Garrido
authors.forename: Mathias
authors.initials: M
authors.lastname: Bähr
authors.forename: Sebastian
authors.initials: S
authors.lastname: Kügler
authors.forename: Uwe
authors.initials: U
authors.lastname: Michel
mesh_terms: D001483:Base Sequence; D020869:Gene Expression Profiling / Q000379:methods*; D020868:Gene Silencing; D018390:Gene Targeting / Q000379:methods*; D005822:Genetic Vectors / Q000235:genetics; D049452:Green Fluorescent Proteins / Q000235:genetics* / Q000378:metabolism; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic / Q000235:genetics*; D034622:RNA Interference; D017423:Sequence Analysis, RNA / Q000379:methods; D013050:Spectrometry, Fluorescence / Q000379:methods*
chemical_list: D049452:Green Fluorescent Proteins