title: Branchpoint expansion in a fully complementary three-way DNA junction.
abstract: Branched nucleic acid molecules serve as key intermediates in DNA replication, recombination, and repair; architectural elements in RNA; and building blocks and functional components for nanoscience applications. Using a combination of high-resolution single-molecule FRET, time-resolved spectroscopy, and molecular modeling, we have probed the local and global structure of a DNA three-way junction (3WJ) in solution. We found that it adopts a Y-shaped, pyramidal structure, in which the bases adjacent to the branchpoint are unpaired, despite the full Watson-Crick complementarity of the molecule. The unpairing allows a nanoscale cavity to form at the junction center. Our structure accounts for earlier observations made of the structure, flexibility, and reactivity of 3WJs. We anticipate that these results will guide the development of new DNA-based supramolecular receptors and nanosystems.
authors.affiliation: The School of Chemistry, Alan Turing Building, The University of Manchester, Oxford Road, Manchester M13 9PL, UK.
authors.forename: Tara
authors.initials: T
authors.lastname: Sabir
authors.forename: Anita
authors.initials: A
authors.lastname: Toulmin
authors.forename: Long
authors.initials: L
authors.lastname: Ma
authors.forename: Anita C
authors.initials: AC
authors.lastname: Jones
authors.forename: Peter
authors.initials: P
authors.lastname: McGlynn
authors.forename: Gunnar F
authors.initials: GF
authors.lastname: Schröder
authors.forename: Steven W
authors.initials: SW
authors.lastname: Magennis
mesh_terms: D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D031541:Fluorescence Resonance Energy Transfer / Q000379:methods; D006860:Hydrogen Bonding; D007477:Ions; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D036103:Nanotechnology / Q000379:methods; D009690:Nucleic Acid Conformation; D009696:Nucleic Acids; D009711:Nucleotides / Q000737:chemistry; D012313:RNA / Q000737:chemistry; D015203:Reproducibility of Results; D013053:Spectrophotometry / Q000379:methods
chemical_list: D007477:Ions; D009696:Nucleic Acids; D009711:Nucleotides; D012313:RNA; D004247:DNA