Thermodynamics of folding a pseudoknotted mRNA fragment

Journal of Molecular Biology
T C Gluick, D E Draper

Abstract

A sequence in the leader and first gene of the Escherichia coli alpha mRNA folds into a complex pseudoknot structure that is required for binding of a translational repressor. The thermal denaturation of a 112 nt RNA containing this structure has been followed by calorimetry and UV hyperchromicity. To determine the partially folded intermediates in unfolding, the denaturation of 13 mutants and of several fragments with successive deletions of helices were investigated as well. An unfolding pathway with seven states is proposed as the simplest mechanism that accounts for the data, and has several implications. (1) The lowest temperature transition appears only in the presence of moderate concentrations of Mg2+ or high concentrations of K+ (delta H approximately 45 kcal/mol), and is the unfolding of tertiary structures, rather than secondary structure. Under some conditions it is destabilized by increasing salt concentration. (2) Two of the intermediates unfolding at higher temperature must have non-canonical or tertiary interactions in addition to the known secondary structure. (3) Two alternative structures compete for formation of the complete pseudoknot, and form as the pseudoknot unfolds. Thus structures not present in the c...Continue Reading

Citations

Jun 23, 2000·RNA·D Thirumalai, S A Woodson
May 1, 1996·Nature Structural Biology·D E Draper
Dec 21, 2006·Nucleic Acids Research·Xiaolu Huang, Hesham Ali
Jan 6, 2010·Nucleic Acids Research·Stéfan Engelen, Fariza Tahi
Jan 1, 1997·Annual Review of Biophysics and Biomolecular Structure·P Brion, E Westhof
Jul 20, 1999·Annual Review of Biophysics and Biomolecular Structure·A R Ferré-D'Amaré, J A Doudna
May 20, 2006·Nucleic Acids Research·Song Cao, Shi-Jie Chen
Jan 19, 2000·Proceedings of the National Academy of Sciences of the United States of America·S J Chen, K A Dill
Nov 26, 2015·Journal of the American Chemical Society·Xinyue ZhangLi-Qun Gu
Aug 3, 2005·Journal of Theoretical Biology·Hamed Shateri NajafabadiSetareh Sadat Banihosseini
May 5, 1998·Folding & Design·O Galzitskaya, A V Finkelstein
Jul 6, 2000·Molecular Cell·A A Andersen, R A Collins
Jul 25, 1998·Journal of Molecular Biology·J Pan, S A Woodson
Jan 7, 1998·Journal of Molecular Biology·Y V Bukhman, D E Draper
Jan 24, 2006·Biopolymers·Peter J Mikulecky, Andrew L Feig
Apr 17, 2002·Journal of Molecular Biology·Durga M ChadalavadaPhilip C Bevilacqua
Aug 31, 2000·Journal of Molecular Biology·R Shiman, D E Draper
Feb 2, 1999·Journal of Molecular Biology·E Rivas, S R Eddy
Apr 1, 1996·Trends in Biochemical Sciences·D E Draper
Dec 18, 2003·The Journal of Biological Chemistry·Tapas K SenguptaEleanor K Spicer
Oct 23, 1998·Nature·A R Ferré-D'AmaréJ A Doudna
Oct 1, 1995·Journal of Biomolecular Structure & Dynamics·S A WhiteM E Rauch
Sep 29, 1995·The Journal of Biological Chemistry·A M Baker, D E Draper
Jun 22, 2002·The Journal of Biological Chemistry·Philip PinheiroJames A McClellan
May 21, 2015·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Tristan CragnoliniSamuela Pasquali
Jul 30, 2019·Biophysical Journal·Ofer KimchiLucy J Colwell
Mar 17, 2007·Biochemistry·Joshua M BlosePhilip C Bevilacqua
Jun 1, 1995·Current Opinion in Structural Biology·A M Pyle, J B Green
Mar 31, 2005·Journal of the American Chemical Society·Kevin A WilkinsonKevin M Weeks
Dec 8, 1998·Biochemistry·J M Bevilacqua, P C Bevilacqua

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