title: Folding of the natural hammerhead ribozyme is enhanced by interaction of auxiliary elements.
abstract: It has been shown that the activity of the hammerhead ribozyme at microM magnesium ion concentrations is markedly increased by the inclusion of loops in helices I and II. We have studied the effect of such loops on the magnesium ion-induced folding of the ribozyme, using fluorescence resonance energy transfer. We find that with the loops in place, folding into the active conformation occurs in a single step, in the microM range of magnesium ion concentration. Disruption of the loop-loop interaction leads to a reversion to two-step folding, with the second stage requiring mM concentrations of magnesium ion. Sodium ions also promote the folding of the natural form of the ribozyme at high concentrations, but the folding occurs as a two-stage process. The loops clearly act as important auxiliary elements in the function of the ribozyme, permitting folding to occur efficiently under physiological conditions.
authors.affiliation: Cancer Research UK Nucleic Acid Structure Research Group, Department of Biochemistry, The University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, United Kingdom.
authors.forename: J Carlos
authors.initials: JC
authors.lastname: Penedo
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Wilson
authors.forename: Sumedha D
authors.initials: SD
authors.lastname: Jayasena
authors.forename: Anastasia
authors.initials: A
authors.lastname: Khvorova
authors.forename: David M J
authors.initials: DM
authors.lastname: Lilley
mesh_terms: D031541:Fluorescence Resonance Energy Transfer; D008274:Magnesium / Q000378:metabolism; D009690:Nucleic Acid Conformation; D016337:RNA, Catalytic / Q000737:chemistry / Q000378:metabolism*
chemical_list: D016337:RNA, Catalytic; C427204:hammerhead ribozyme; D008274:Magnesium