title: Cationic modified nucleic acids for use in DNA hairpins and parallel triplexes.
abstract: Non-nucleosidic DNA monomers comprising partially protonated amines at low pH have been designed and synthesized. The modifications were incorporated into DNA oligonucleotides via standard DNA phosphoramidite synthesis. The ability of cationic modifications to stabilize palindromic DNA hairpins and parallel triplexes were evaluated using gel electrophoresis, circular dichroism and thermal denaturation measurements. The non-nucleosidic modifications were found to increase the thermal stability of palindromic hairpins at pH 8.0 as compared with a nucleosidic tetraloop (TCTC). Incorporation of modifications at the 5'-end of a triplex forming oligonucleotide resulted in a significant increase in thermal stability at low pH when the modifications were placed as the 5'-dangling end.
authors.affiliation: Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark. bom@ifk.sdu.dk
authors.forename: Niels
authors.initials: N
authors.lastname: Bomholt
authors.forename: Vyacheslav V
authors.initials: VV
authors.lastname: Filichev
authors.forename: Erik B
authors.initials: EB
authors.lastname: Pedersen
mesh_terms: D002412:Cations / Q000737:chemistry; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D004591:Electrophoresis, Polyacrylamide Gel; D006863:Hydrogen-Ion Concentration; D055029:Inverted Repeat Sequences; D009682:Magnetic Resonance Spectroscopy; D008967:Molecular Biology / Q000379:methods*; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009841:Oligonucleotides / Q000138:chemical synthesis* / Q000378:metabolism; D009943:Organophosphorus Compounds / Q000737:chemistry* / Q000378:metabolism
chemical_list: D002412:Cations; D009841:Oligonucleotides; D009943:Organophosphorus Compounds; C434331:phosphoramidite; D004247:DNA