title: Global structure of three-way DNA junctions with and without additional unpaired bases: a fluorescence resonance energy transfer analysis.
abstract: The structure of three-way DNA junctions with and without extrahelical adenine nucleotides in one strand at the branch point of the junction (i.e., An bulges with n = 0, 1, 2, and 3) has been investigated by fluorescence resonance energy transfer. The structure of the junction without bulged nucleotides was found to have a symmetric trigonal geometry. With bulges, the arrangement of the arms becomes asymmetrical. The energy transfer results suggest a model of bulged junctions where the angle between two of the arms is significantly smaller than between the other two pairs of arms. The acute angle becomes smaller as the number of nucleotides in the bulge increases. The FRET efficiencies of the junctions are the same in the presence of Mg++ and Na+ ions.
authors.affiliation: Max-Planck-Institut für biophysikalische Chemie, Abteilung Molekulare Biologie, Göttingen, Germany.
authors.forename: F
authors.initials: F
authors.lastname: Stühmeier
authors.forename: J B
authors.initials: JB
authors.lastname: Welch
authors.forename: A I
authors.initials: AI
authors.lastname: Murchie
authors.forename: D M
authors.initials: DM
authors.lastname: Lilley
authors.forename: R M
authors.initials: RM
authors.lastname: Clegg
mesh_terms: D001482:Base Composition; D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D004735:Energy Transfer; D019793:Fluorescein; D005456:Fluorescent Dyes; D009690:Nucleic Acid Conformation; D012235:Rhodamines; D012965:Sodium Chloride; D012996:Solutions; D013050:Spectrometry, Fluorescence
chemical_list: D005456:Fluorescent Dyes; D012235:Rhodamines; D012996:Solutions; D012965:Sodium Chloride; C005358:tetramethylrhodamine; D004247:DNA; D019793:Fluorescein