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 variation

SUBMITTER: Mustoe AM 

PROVIDER: S-EPMC3258142 | biostudies-literature | 2012 Jan

REPOSITORIES: biostudies-literature