title: High-affinity triplex targeting of double stranded DNA using chemically modified peptide nucleic acid oligomers.
abstract: While sequence-selective dsDNA targeting by triplex forming oligonucleotides has been studied extensively, only very little is known about the properties of PNA-dsDNA triplexes--mainly due to the competing invasion process. Here we show that when appropriately modified using pseudoisocytosine substitution, in combination with (oligo)lysine or 9-aminoacridine conjugation, homopyrimidine PNA oligomers bind complementary dsDNA targets via triplex formation with (sub)nanomolar affinities (at pH 7.2, 150 mM Na(+)). Binding affinity can be modulated more than 1000-fold by changes in pH, PNA oligomer length, PNA net charge and/or by substitution of pseudoisocytosine for cytosine, and conjugation of the DNA intercalator 9-aminoacridine. Furthermore, 9-aminoacridine conjugation also strongly enhanced triplex invasion. Specificity for the fully matched target versus one containing single centrally located mismatches was more than 150-fold. Together the data support the use of homopyrimidine PNAs as efficient and sequence selective tools in triplex targeting strategies under physiological relevant conditions.
authors.affiliation: Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen 2200-N, Denmark.
authors.forename: Mads E
authors.initials: ME
authors.lastname: Hansen
authors.forename: Thomas
authors.initials: T
authors.lastname: Bentin
authors.forename: Peter E
authors.initials: PE
authors.lastname: Nielsen
mesh_terms: D000585:Aminacrine / Q000737:chemistry; D001483:Base Sequence; D003596:Cytosine / Q000031:analogs & derivatives / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D006863:Hydrogen-Ion Concentration; D007364:Intercalating Agents / Q000737:chemistry; D020135:Peptide Nucleic Acids / Q000737:chemistry*
chemical_list: D007364:Intercalating Agents; D020135:Peptide Nucleic Acids; C465235:pseudoisocytosine; C051802:triplex DNA; D000585:Aminacrine; D003596:Cytosine; D004247:DNA