mRNAs deregulated by GFP siRNA contain short sequences perfectly matched to the sense or antisense strand of GFP siRNA. In order to shed light on the molecular mechanism of sequence-specific off-target effects, we analyzed the mRNAs modulated after transfection of GFP siRNA for sequence homology to the transfected siRNA molecules. The number of perfect matches with a homology length of at least 8 bp was significantly higher using the proper GFP siRNA sequences as compared to the shuffled siRNA sequences.
Tschuch et al. BMC Molecular Biology 2008 9:60 doi:10.1186/1471-2199-9-60