Binding of HIV-1 TAR mRNA to a peptide nucleic acid oligomer and its conjugates with metal-ion-binding multidentate ligands

  • Matthew J. Belousoff
  • Gilles Gasser
  • Bim Graham
  • Yitzhak Tor
  • Leone Spiccia
Original Paper


A peptide nucleic acid (PNA) oligomer and a series of PNA conjugates featuring covalently attached pendant 1,4,7,10-tetraazacyclododecane (cyclen) or bis((pyridin-2-yl)methyl)amine (DPA) moieties have been synthesized that are complementary to regions of the HIV-1 TAR messenger RNA stem-loop. Thermal denaturation studies, in conjunction win with native gel shift assays, suggest that the PNAs “invade” TAR to produce a mixture of two 1:1 PNA–TAR adducts, tentatively assigned as an “open-duplex” structure, in which the TAR stem-loop dissociates and the PNA hybridizes with its RNA complement via Watson–Crick base-pairing, and a triplex-type structure, in which the initially displaced RNA segment is bound to the PNA:RNA duplex through Hoogsteen base-pairing. Thermal denaturation experiments with the TAR sequence and single-stranded RNA and DNA oligonucleotides, both in the presence and in the absence of Zn2+ ions, show that the introduction of cyclen or DPA ligand arms into the PNA oligomer leads to a small but reproducible increase in the T m values. This is attributed to hydrogen-bonding and/or electrostatic interactions between protonated forms of cyclen/DPA and the cognate RNA or DNA oligonucleotide targets. Contrary to expectations, the addition of Zn2+ ions did not further enhance duplex formation through binding of Zn(II)–cyclen or Zn(II)–DPA moieties to the complementary RNA or DNA. Native gel shift assays further confirmed the stability increase of the metal-free cyclen- and DPA-modified PNA hybrids as compared with a control PNA sequence.


Peptide nucleic acids Macrocycle peptide nucleic acid hybrids Bis((pyridin-2-yl)methyl)amine–peptide nucleic acid hybrids Zinc(II) complexes Targeting HIV-1 TAR stem-loop 



This work was supported by the Swiss National Science Foundation and the Australian Research Council (ARC) through the Australian Centre for Electromaterials Science (for L.S.) and (for Y.T.) the National Institutes of Health (grants number AI 47673 and GM 069773). G.G. was the recipient of a Swiss Fellowship for Prospective Researchers Grant (PBNE2-106771). M.J.B. was the recipient of an Australian Postgraduate Award and was supported by a Fulbright Fellowship. We are grateful to S.J. Langford for access to the PNA synthesizer.

Supplementary material

775_2008_448_MOESM1_ESM.pdf (2.3 mb)
Supplementary material (PDF 2.26 MB)


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Copyright information

© SBIC 2008

Authors and Affiliations

  1. 1.School of ChemistryMonash UniversityClaytonAustralia
  2. 2.Department of Chemistry and BiochemistryUniversity of California, San DiegoLa JollaUSA
  3. 3.Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical SciencesMonash UniversityParkvilleAustralia

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