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A screen of chemical modifications identifies position-specific modification by UNA to most potently reduce siRNA off-target effects

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avis › Tidsskriftartikel › Forskning › peer review

DOI

  • Jesper Bertram Bramsen
  • Malgorzata M Pakula
    • ,
  • Thomas B Hansen
    • ,
  • Claus Bus
  • Niels Langkjær, Syddansk Universitet, Danmark
  • Dalibor Odadzic, Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Tyskland
  • Romualdas Smicius, Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Tyskland
  • Suzy L Wengel, RiboTask ApS, Danmark
  • Jyoti Chattopadhyaya, Uppsala University, Sverige
  • Joachim W Engels, Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Tyskland
  • Piet Herdewijn, Rega Institute for Medical Research KU Leuven, Holland
  • Jesper Wengel, Syddansk Universitet, Danmark
  • Jørgen Kjems
Small interfering RNAs (siRNAs) are now established as the preferred tool to inhibit gene function in mammalian cells yet trigger unintended gene silencing due to their inherent miRNA-like behavior. Such off-target effects are primarily mediated by the sequence-specific interaction between the siRNA seed regions (position 2-8 of either siRNA strand counting from the 5'-end) and complementary sequences in the 3'UTR of (off-) targets. It was previously shown that chemical modification of siRNAs can reduce off-targeting but only very few modifications have been tested leaving more to be identified. Here we developed a luciferase reporter-based assay suitable to monitor siRNA off-targeting in a high throughput manner using stable cell lines. We investigated the impact of chemically modifying single nucleotide positions within the siRNA seed on siRNA function and off-targeting using 10 different types of chemical modifications, three different target sequences and three siRNA concentrations. We found several differently modified siRNAs to exercise reduced off-targeting yet incorporation of the strongly destabilizing unlocked nucleic acid (UNA) modification into position 7 of the siRNA most potently reduced off-targeting for all tested sequences. Notably, such position-specific destabilization of siRNA-target interactions did not significantly reduce siRNA potency and is therefore well suited for future siRNA designs especially for applications in vivo where siRNA concentrations, expectedly, will be low
OriginalsprogEngelsk
TidsskriftNucleic Acids Research
Vol/bind38
Nummer17
Sider (fra-til)5761-5773
Antal sider13
ISSN0305-1048
DOI
StatusUdgivet - 2010

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