Targeting of repeated sequences unique to a gene results in significant increases in antisense oligonucleotide potency

PLoS One. 2014 Oct 15;9(10):e110615. doi: 10.1371/journal.pone.0110615. eCollection 2014.

Abstract

A new strategy for identifying potent RNase H-dependent antisense oligonucleotides (ASOs) is presented. Our analysis of the human transcriptome revealed that a significant proportion of genes contain unique repeated sequences of 16 or more nucleotides in length. Activities of ASOs targeting these repeated sites in several representative genes were compared to those of ASOs targeting unique single sites in the same transcript. Antisense activity at repeated sites was also evaluated in a highly controlled minigene system. Targeting both native and minigene repeat sites resulted in significant increases in potency as compared to targeting of non-repeated sites. The increased potency at these sites is a result of increased frequency of ASO/RNA interactions which, in turn, increases the probability of a productive interaction between the ASO/RNA heteroduplex and human RNase H1 in the cell. These results suggest a new, highly efficient strategy for rapid identification of highly potent ASOs.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Cell Line
  • Gene Expression
  • Genes, Reporter
  • Humans
  • Oligonucleotides, Antisense / genetics*
  • Oligonucleotides, Antisense / metabolism
  • RNA Splicing
  • Receptors, Glucagon / genetics
  • Repetitive Sequences, Nucleic Acid*
  • Ribonuclease H / metabolism
  • Transcriptome

Substances

  • Oligonucleotides, Antisense
  • Receptors, Glucagon
  • Ribonuclease H

Grants and funding

This work was supported by Isis Pharmaceuticals. The funder provided support in the form of salaries for authors TAV, SMF, HHB, AW, and STC, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section.