Methods for determining specificity of rna silencing and for genetic analysis of the silenced gene or protein - Patents

Methods for determining specificity of rna silencing and for genetic analysis of the silenced gene or protein

Agent: Dann, Dorfman, Herrell & Skillman - Philadelphia, PA, US
Inventors: Daniel F. Klessig, Dhirendra Kumar
Applicaton #: 20060287272
Class: 514044000 (USPTO)
12/21/06
Methods and kits for determining the specificity of siRNAs for their targets are provided. Also provided is a method for performing genetic analysis of the target protein or gene using different versions of a synthetic gene to complement the phenotype induced by RNAi-mediated silencing of the target protein and/or gene of interest. Finally, a method for treating genetic disorders associated with production of mutated proteins is also disclosed.
FIELD OF THE INVENTION
[0003] The present invention relates to the fields of molecular biology, genetics and regulation of gene expression. More specifically the invention relates to methods for assessing the specificity of RNA silencing in plants and other organisms and for genetic analysis of the silenced gene or protein. Method are also provided for complementing genetic defects using synthetic nucleic acid constructs encoding wild type proteins which are not subject to RNAi.
BACKGROUND OF THE INVENTION
[0004] Several publications and patent documents are cited throughout this application in order to more fully describe the state of the art to which this invention pertains. Each of these citations is incorporated by reference herein.
[0005] RNA interference (RNAi) relates to a mechanism of selective gene silencing mediated through short interfering RNA (siRNA) and may be a general feature of gene regulation and expression in most, if not all, eukaryotes. RNAi technology has made pan-genomic functional gene analysis a reality and is a powerful strategy to quickly identify and validate new targets for therapeutic invention. In 2002, Science named RNAi Breakthrough of the Year, while Fortune in 2003 proclaimed it biotech's next billion dollar breakthrough. Despite the early success of RNAi, recent reports suggest that siRNAs are not always as specific as was first assumed (1,2). The siRNA silencing of non-targeted genes, termed off-target effects (OTE), often appear to be caused by silencing target gene homologs and/or other genes that share partial sequence complementarity to the siRNA (3). Since some base pair mismatches are tolerated in this type of OTE, it is thought that the siRNA functions as a micro RNA (miRNA) and represses translation of transcripts with partial homology (4,5). This type of OTE decreases protein, but not necessarily mRNA, concentration of the non-targeted gene. Unfortunately, the lack of siRNA specificity is often assessed through gene expression profiling with microarrays, an approach that does not detect OTEs caused by altered translation. A second and more controversial possible cause of OTE is siRNA-mediated activation of the interferon pathway.
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