title: Alternative conformations of a nucleic acid four-way junction.
abstract: A crystal structure of a 108 nucleotide RNA-DNA complex containing a four-way junction was solved at 3.1 A resolution. The structure of the junction differs substantially from the "stacked-X" conformation observed previously, due to a 135 degrees rotation of the branches. Comparison of the two conformers provides insight into the factors contributing to the flexibility of four-way junctions. The stacked-X conformation maximizes base-stacking but causes unfavorable repulsion between phosphate groups, whereas the 135 degrees -rotated "crossed" conformation minimizes electrostatic clashes at the expense of reduced base-stacking. Despite the large rotation of the branches, both junction structures exhibit an antiparallel arrangement of the continuous strands and opposite polarity of the crossover strands.
authors.affiliation: Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA.
authors.forename: J
authors.initials: J
authors.lastname: Nowakowski
authors.forename: P J
authors.initials: PJ
authors.lastname: Shim
authors.forename: C D
authors.initials: CD
authors.lastname: Stout
authors.forename: G F
authors.initials: GF
authors.lastname: Joyce
mesh_terms: D020029:Base Pairing / Q000235:genetics; D001483:Base Sequence; D003434:Crossing Over, Genetic / Q000235:genetics*; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D021881:DNA, Catalytic; D004277:DNA, Single-Stranded / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D007536:Isomerism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009692:Nucleic Acid Heteroduplexes / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D010710:Phosphates / Q000378:metabolism; D018583:Pliability; D012313:RNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D012399:Rotation; D055672:Static Electricity
chemical_list: D021881:DNA, Catalytic; D004277:DNA, Single-Stranded; D009692:Nucleic Acid Heteroduplexes; D010710:Phosphates; C402582:RNA-cleaving DNA 10-23; D012313:RNA; D004247:DNA