title: New insights into the fundamental role of topological constraints as a determinant of two-way junction conformation.
abstract: Recent studies have shown that topological constraints encoded at the RNA secondary structure level involving basic steric and stereochemical forces can significantly restrict the orientations sampled by helices across two-way RNA junctions. Here, we formulate these topological constraints in greater quantitative detail and use this topological framework to rationalize long-standing but poorly understood observations regarding the basic behavior of RNA two-way junctions. Notably, we show that the asymmetric nature of the A-form helix and the finite length of a bulge provide a physical basis for the experimentally observed directionality and bulge-length amplitude dependence of bulge induced inter-helical bends. We also find that the topologically allowed space can be modulated by variations in sequence, particularly with the addition of non-canonical GU base pairs at the junction, and, surprisingly, by the length of the 5' and 3' helices. A survey of two-way RNA junctions in the protein data bank confirms that junction residues have a strong preference to adopt looped-in, non-canonically base-paired conformations, providing a route for extending our bulge-directed framework to internal loop motifs and implying a simplified link between secondary and tertiary structure. Finally, our results uncover a new simple mechanism for coupling junction-induced topological constraints with tertiary interactions.
authors.affiliation: Departments of Chemistry & Biophysics, The University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109-1055, USA.
authors.forename: Anthony M
authors.initials: AM
authors.lastname: Mustoe
authors.forename: Maximillian H
authors.initials: MH
authors.lastname: Bailor
authors.forename: Robert M
authors.initials: RM
authors.lastname: Teixeira
authors.forename: Charles L
authors.initials: CL
authors.lastname: Brooks
authors.forename: Hashim M
authors.initials: HM
authors.lastname: Al-Hashimi
mesh_terms: D020029:Base Pairing; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D012399:Rotation
chemical_list: D012313:RNA