Thermodynamics of RNA unfolding: stabilization of a ribosomal RNA tertiary structure by thiostrepton and ammonium ion

Journal of Molecular Biology
D E DraperL G Laing

Abstract

RNAs with interesting secondary and tertiary structures tend to melt in several broad and overlapping transitions over a wide temperature range, and it has been consequently difficult to resolve the thermodynamics of individual unfolding steps. In the case that a ligand selectively binds a single folded state of the RNA, it is possible to obtain reliable thermodynamic parameters for both RNA unfolding and RNA-ligand binding simply from the hyperchromicity of RNA denaturation. The analysis procedure involves fitting a three-dimensional surface to absorbance data collected as a function of both temperature and ligand concentration. Analysis of the unfolding of a fragment of the large subunit ribosomal RNA (Escherichia coli sequence 1051 to 1109) is presented; both an antibiotic (thiostrepton) and ammonium ion specifically stabilize a tertiary structure within this RNA. A consistent set of thermodynamic parameters (delta H and tm) for the first two sequentially linked unfolding transitions is obtained from the experiments, and the binding constants obtained for the two ligands are consistent with other independent measurements. The approach is applicable to a variety of RNAs that specifically bind proteins, antibiotics, ions or ot...Continue Reading

Citations

May 24, 2006·Biochemistry·Corina MaederDavid E Draper
Sep 10, 1998·Nature Structural Biology·L Jiang, D J Patel
Jul 15, 1996·Nucleic Acids Research·Y X WangD E Draper
Aug 15, 1997·Nucleic Acids Research·E J Maglott, G D Glick
Aug 18, 1999·Proceedings of the National Academy of Sciences of the United States of America·M V RodninaW Wintermeyer
Jan 7, 1998·Journal of Molecular Biology·Y V Bukhman, D E Draper
Oct 20, 2004·The Journal of Biological Chemistry·William S BowenWalter E Hill
Dec 17, 2008·Chembiochem : a European Journal of Chemical Biology·Sebastian SchoofHans-Dieter Arndt
Jun 24, 2005·The Journal of Biological Chemistry·Sarae L BauschDavid E Draper
Oct 16, 2013·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Pradeep Bhadola, N Deo
Apr 23, 2008·Current Protocols in Nucleic Acid Chemistry·E J Maglott, G D Glick
Jan 1, 1997·Progress in Biophysics and Molecular Biology·M G Wallis, R Schroeder
Jun 2, 1995·Journal of Molecular Biology·Y Xing, D E Draper
Mar 26, 1999·Biochemistry·D GuhaThakurta, D E Draper

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