title: Intercalating nucleic acids (INAs) with insertion of N-(pyren-1-ylmethyl)-(3R,4R)-4-(hydroxymethyl)pyrrolidin-3-ol. DNA (RNA) duplex and DNA three-way junction stabilities.
abstract: N-(Pyren-1-ylmethyl)-(3R,4R)-4-(hydroxymethyl)pyrrolidin-3-ol was synthesised from (3R,4R)-4-(hydroxymethyl)pyrrolidin-3-ol and (3R,4S)-4-[(1S)-1,2-dihydroxyethyl] pyrrolidin-3-ol using alkylation with 1-(chloromethyl)pyrene or reductive amination with pyrene-1-carbaldehyde and NaCNBH3. The incorporation of N-(pyren-1-ylmethyl)azasugar moiety into oligodeoxynucleotides (ODN) as a bulge to form an intercalating nucleic acid (INA) induced a slight destabilization of INA-DNA duplex, whereas the INA-RNA duplex was strongly destabilized and 9 degrees C difference per modification in thermal stability between INA-DNA over INA-RNA duplexes was observed. The stabilization of a DNA three way junction (TWJ) was improved when the intercalator moiety was inserted into the junction region as a bulge.
authors.affiliation: Nucleic Acid Center, Department of Chemistry, University of Southern Denmark, DK-5230 Odense M, Denmark.
authors.forename: Vyacheslav V
authors.initials: VV
authors.lastname: Filichev
authors.forename: Erik B
authors.initials: EB
authors.lastname: Pedersen
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D007364:Intercalating Agents / Q000494:pharmacology*; D009682:Magnetic Resonance Spectroscopy; D008956:Models, Chemical; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009693:Nucleic Acid Hybridization; D009696:Nucleic Acids / Q000737:chemistry*; D009841:Oligonucleotides / Q000737:chemistry; D011721:Pyrenes / Q000138:chemical synthesis*; D011759:Pyrrolidines / Q000138:chemical synthesis*; D012313:RNA / Q000737:chemistry*; D013053:Spectrophotometry; D013696:Temperature
chemical_list: D007364:Intercalating Agents; C480173:N-(pyren-1-ylmethyl)-(3R,4R)-4-(hydroxymethyl)pyrrolidin-3-ol; D009696:Nucleic Acids; D009841:Oligonucleotides; D011721:Pyrenes; D011759:Pyrrolidines; D012313:RNA; D004247:DNA