Hydroxyproline-based DNA mimics provide an efficient gene silencing in vitro and in vivo

Nucleic Acids Res. 2006 May 2;34(8):2247-57. doi: 10.1093/nar/gkl249. Print 2006.


To be effective, antisense molecules should be stable in biological fluids, non-toxic, form stable and specific duplexes with target RNAs and readily penetrate through cell membranes without non-specific effects on cell function. We report herein that negatively charged DNA mimics representing chiral analogues of peptide nucleic acids with a constrained trans-4-hydroxy-N-acetylpyrrolidine-2-phosphonate backbone (pHypNAs) meet these criteria. To demonstrate this, we compared silencing potency of these compounds with that of previously evaluated as efficient gene knockdown molecules hetero-oligomers consisting of alternating phosphono-PNA monomers and PNA-like monomers based on trans-4-hydroxy-L-proline (HypNA-pPNAs). Antisense potential of pHypNA mimics was confirmed in a cell-free translation assay with firefly luciferase as well as in a living cell assay with green fluorescent protein. In both cases, the pHypNA antisense oligomers provided a specific knockdown of a target protein production. Confocal microscopy showed that pHypNAs, when transfected into living cells, demonstrated efficient cellular uptake with distribution in the cytosol and nucleus. Also, the high potency of pHypNAs for down-regulation of Ras-like GTPase Ras-dva in Xenopus embryos was demonstrated in comparison with phosphorodiamidate morpholino oligomers. Therefore, our data suggest that pHypNAs are novel antisense agents with potential widespread in vitro and in vivo applications in basic research involving live cells and intact organisms.

MeSH terms

  • Animals
  • Biological Transport
  • Cell-Free System
  • Cells, Cultured
  • DNA / chemistry
  • Gene Silencing*
  • Hydroxyproline / chemistry*
  • Molecular Mimicry
  • Monomeric GTP-Binding Proteins / genetics
  • Oligonucleotides, Antisense / chemical synthesis
  • Oligonucleotides, Antisense / chemistry*
  • Oligonucleotides, Antisense / metabolism
  • Organophosphonates / chemistry*
  • Peptide Nucleic Acids / chemical synthesis
  • Peptide Nucleic Acids / chemistry*
  • Peptide Nucleic Acids / metabolism
  • Protein Biosynthesis
  • Xenopus
  • Xenopus Proteins / genetics


  • Oligonucleotides, Antisense
  • Organophosphonates
  • Peptide Nucleic Acids
  • Xenopus Proteins
  • DNA
  • Monomeric GTP-Binding Proteins
  • ras-dva1 protein, Xenopus
  • Hydroxyproline