title: Kinking of DNA and RNA helices by bulged nucleotides observed by fluorescence resonance energy transfer.
abstract: Fluorescence resonance energy transfer (FRET) has been used to demonstrate the bending of DNA and RNA helices for three series of double-stranded molecules containing bulge loops of unopposed adenosine nucleotides (An, n = 0-9). Fluorescein and rhodamine were covalently attached to the 5' termini of the two component strands. Three different methods were applied to measure the FRET efficiencies. The extent of energy transfer within each series increases as the number of bulged nucleotides varies from 1 to 7, indicating a shortening of the end-to-end distance. This is consistent with a bending of DNA and RNA helices that is greater for larger bulges. The FRET efficiency for DNA molecules with A9 bulges is lower than the efficiency for the corresponding A7 bulged molecules, although the A9 molecules exhibit increased electrophoretic retardation. Ranges of bending angles can be estimated from the FRET results.
authors.affiliation: Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttengen, Federal Republic of Germany.
authors.forename: C
authors.initials: C
authors.lastname: Gohlke
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: D000227:Adenine Nucleotides / Q000737:chemistry; D001483:Base Sequence; D004247:DNA / Q000737:chemistry / Q000648:ultrastructure*; D004735:Energy Transfer; D005454:Fluorescence Polarization; D066298:In Vitro Techniques; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D012313:RNA / Q000737:chemistry / Q000648:ultrastructure*; D013050:Spectrometry, Fluorescence
chemical_list: D000227:Adenine Nucleotides; D009838:Oligodeoxyribonucleotides; D012313:RNA; D004247:DNA