Binding of HIV-1 TAR mRNA to a peptide nucleic acid oligomer and its conjugates with metal-ion-binding multidentate ligands.
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 Zn(2+) 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 Zn(2+) 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.
Belousoff
Matthew J
MJ
School of Chemistry, Monash University, Clayton, VIC, 3800, Australia.
Gasser
Gilles
G
Graham
Bim
B
Tor
Yitzhak
Y
Spiccia
Leone
L
D001483:Base Sequence; D001665:Binding Sites; D000080027:Cyclams; D016325:HIV Long Terminal Repeat / Q000235:genetics*; D006571:Heterocyclic Compounds / Q000737:chemistry*; D006860:Hydrogen Bonding; D008024:Ligands; D015394:Molecular Structure; D009942:Organometallic Compounds / Q000138:chemical synthesis / Q000737:chemistry; D020135:Peptide Nucleic Acids / Q000138:chemical synthesis / Q000737:chemistry* / Q000378:metabolism; D011489:Protein Denaturation; D011725:Pyridines / Q000737:chemistry*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism*; D012367:RNA, Viral / Q000235:genetics / Q000378:metabolism*; D013237:Stereoisomerism; D013696:Temperature; D015032:Zinc / Q000737:chemistry*
D000080027:Cyclams; D006571:Heterocyclic Compounds; D008024:Ligands; D009942:Organometallic Compounds; D020135:Peptide Nucleic Acids; D011725:Pyridines; D012333:RNA, Messenger; D012367:RNA, Viral; C038072:cyclen; D015032:Zinc