title: Structure of the three-way helical junction of the hepatitis C virus IRES element.
abstract: The hepatitis C virus internal ribosome entry site (IRES) element contains a three-way junction that is important in the overall RNA conformation, and for its role in the internal initiation of translation. The junction also illustrates some important conformational principles in the folding of three-way helical junctions. It is formally a 3HS(4) junction, with the possibility of two alternative stacking conformers. However, in principle, the junction can also undergo two steps of branch migration that would form 2HS(1)HS(3) and 2HS(2)HS(2) junctions. Comparative gel electrophoresis and ensemble fluorescence resonance energy transfer (FRET) studies show that the junction is induced to fold by the presence of Mg(2+) ions in low micromolar concentrations, and suggest that the structure adopted is based on coaxial stacking of the two helices that do not terminate in a hairpin loop (i.e., helix IIId). Single-molecule FRET studies confirm this conclusion, and indicate that there is no minor conformer present based on an alternative choice of helical stacking partners. Moreover, analysis of single-molecule FRET data at an 8-msec resolution failed to reveal evidence for structural transitions. It seems probable that this junction adopts a single conformation as a unique and stable fold.
authors.affiliation: Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee DD1 5EH, United Kingdom.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Ouellet
authors.forename: Sonya
authors.initials: S
authors.lastname: Melcher
authors.forename: Asif
authors.initials: A
authors.lastname: Iqbal
authors.forename: Yiliang
authors.initials: Y
authors.lastname: Ding
authors.forename: David M J
authors.initials: DM
authors.lastname: Lilley
mesh_terms: D031541:Fluorescence Resonance Energy Transfer; D016174:Hepacivirus / Q000235:genetics* / Q000378:metabolism; D017433:Protein Structure, Secondary / Q000235:genetics; D012270:Ribosomes / Q000235:genetics / Q000378:metabolism*