2'-Fluoro-modified phosphorothioate oligonucleotide can cause rapid degradation of P54nrb and PSF

Nucleic Acids Res. 2015 May 19;43(9):4569-78. doi: 10.1093/nar/gkv298. Epub 2015 Apr 8.

Abstract

Synthetic oligonucleotides are used to regulate gene expression through different mechanisms. Chemical modifications of the backbone of the nucleic acid and/or of the 2' moiety of the ribose can increase nuclease stability and/or binding affinity of oligonucleotides to target molecules. Here we report that transfection of 2'-F-modified phosphorothioate oligonucleotides into cells can reduce the levels of P54nrb and PSF proteins through proteasome-mediated degradation. Such deleterious effects of 2'-F-modified oligonucleotides were observed in different cell types from different species, and were independent of oligonucleotide sequence, positions of the 2'-F-modified nucleotides in the oligonucleotides, method of delivery or mechanism of action of the oligonucleotides. Four 2'-F-modified nucleotides were sufficient to cause the protein reduction. P54nrb and PSF belong to Drosophila behavior/human splicing (DBHS) family. The third member of the family, PSPC1, was also reduced by the 2'-F-modified oligonucleotides. Preferential association of 2'-F-modified oligonucleotides with P54nrb was observed, which is partially responsible for the protein reduction. Consistent with the role of DBHS proteins in double-strand DNA break (DSB) repair, elevated DSBs were observed in cells treated with 2'-F-modified oligonucleotides, which contributed to severe impairment in cell proliferation. These results suggest that oligonucleotides with 2'-F modifications can cause non-specific loss of cellular protein(s).

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cell Line, Tumor
  • DNA Damage
  • Fluorine
  • HeLa Cells
  • Humans
  • Mice
  • Nuclear Matrix-Associated Proteins / metabolism*
  • Nuclear Proteins / metabolism
  • Octamer Transcription Factors / metabolism*
  • Oligonucleotides, Antisense / chemistry
  • Oligonucleotides, Antisense / metabolism*
  • PTB-Associated Splicing Factor
  • Phosphorothioate Oligonucleotides / chemistry
  • Phosphorothioate Oligonucleotides / metabolism*
  • Protein Stability
  • RNA-Binding Proteins / metabolism*

Substances

  • NONO protein, human
  • Nuclear Matrix-Associated Proteins
  • Nuclear Proteins
  • Octamer Transcription Factors
  • Oligonucleotides, Antisense
  • PSPC1 protein, human
  • PTB-Associated Splicing Factor
  • Phosphorothioate Oligonucleotides
  • RNA-Binding Proteins
  • p54nrb protein, mouse
  • Fluorine