title: DNA triplex formation with 5-dimethylaminopropargyl deoxyuridine.
abstract: We have prepared triplex-forming oligonucleotides containing the nucleotide analogue 5-dimethylaminopropargyl deoxyuridine (DMAPdU) in place of thymidine and examined their ability to form intermolecular triple helices by thermal melting and DNase I footprinting studies. The results were compared with those for oligonucleotides containing 5-aminopropargyl-dU (APdU), 5-guanidinopropargyl-dU (GPdU) and 5-propynyl dU (PdU). We find that DMAPdU enhances triplex stability relative to T, though slightly less than the other analogues that bear positive charges (T << PdU < DMAPdU < APdU < GPdU). For oligonucleotides that contain multiple substitutions with DMAPdU dispersed residues are more effective than clustered combinations. DMAPdU will be especially useful as a nucleotide analogue as, unlike APdU and GPdU, the base does not require protection during oligonucleotide synthesis and it can therefore be used with other derivatives that require mild deprotection conditions.
authors.affiliation: School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK.
authors.forename: David A
authors.initials: DA
authors.lastname: Rusling
authors.forename: Guomei
authors.initials: G
authors.lastname: Peng
authors.forename: Natarajan
authors.initials: N
authors.lastname: Srinivasan
authors.forename: Keith R
authors.initials: KR
authors.lastname: Fox
authors.forename: Tom
authors.initials: T
authors.lastname: Brown
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D018983:DNA Footprinting; D003857:Deoxyuridine / Q000031:analogs & derivatives* / Q000737:chemistry; D005453:Fluorescence; D007700:Kinetics; D008744:Methylamines / Q000737:chemistry*; D009691:Nucleic Acid Denaturation; D009841:Oligonucleotides / Q000737:chemistry
chemical_list: C527039:5-dimethylaminopropargyl deoxyuridine; D008744:Methylamines; D009841:Oligonucleotides; C051802:triplex DNA; D004247:DNA; D003857:Deoxyuridine