Gapmer Antisense Oligonucleotides Containing 2′,3′-Dideoxy-2′-fluoro-3′-C-hydroxymethyl-β-d-lyxofuranosyl Nucleotides Display Site-Specific RNase H Cleavage and Induce Gene Silencing

Mathias B. Danielsen, Chenguang Lou, Jolanta Lisowiec-Wachnicka, Anna Pasternak, Per T. Jørgensen, Jesper Wengel*

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

41 Downloads (Pure)

Abstract

Off-target effects remain a significant challenge in the therapeutic use of gapmer antisense oligonucleotides (AONs). Over the years various modifications have been synthesized and incorporated into AONs, however, precise control of RNase H-induced cleavage and target sequence selectivity has yet to be realized. Herein, the synthesis of the uracil and cytosine derivatives of a novel class of 2′-deoxy-2′-fluoro-3′-C-hydroxymethyl-β-d-lyxo-configured nucleotides has been accomplished and the target molecules have been incorporated into AONs. Experiments on exonuclease degradation showed improved nucleolytic stability relative to the unmodified control. Upon the introduction of one or two of the novel 2′-fluoro-3′-C-hydroxymethyl nucleotides as modifications in the gap region of a gapmer AON was associated with efficient RNase H-mediated cleavage of the RNA strand of the corresponding AON:RNA duplex. Notably, a tailored single cleavage event could be engineered depending on the positioning of a single modification. The effect of single mismatched base pairs was scanned along the full gap region demonstrating that the modification enables a remarkable specificity of RNase H cleavage. A cell-based model system was used to demonstrate the potential of gapmer AONs containing the novel modification to mediate gene silencing.

Original languageEnglish
JournalChemistry - A European Journal
Volume26
Issue number6
Pages (from-to)1368-1379
Number of pages12
ISSN0947-6539
DOIs
Publication statusPublished - 27. Jan 2020

Keywords

  • gapmers
  • nucleosides
  • nucleotides
  • RNA cleavage
  • RNase H

Fingerprint Dive into the research topics of 'Gapmer Antisense Oligonucleotides Containing 2′,3′-Dideoxy-2′-fluoro-3′-C-hydroxymethyl-β-d-lyxofuranosyl Nucleotides Display Site-Specific RNase H Cleavage and Induce Gene Silencing'. Together they form a unique fingerprint.

Cite this