Dependence of RNA tertiary structural stability on Mg2+ concentration: interpretation of the Hill equation and coefficient.

Biochemistry
Desirae Leipply, D E Draper

Abstract

The Mg(2+)-induced folding of RNA tertiary structures is readily observed via titrations of RNA with MgCl(2). Such titrations are commonly analyzed using a site binding formalism that includes a parameter, the Hill coefficient n, which is sometimes deemed the number of Mg(2+) ions bound by the native RNA at specific sites. However, the long-range nature of electrostatic interactions allows ions some distance from the RNA to stabilize an RNA structure. A complete description of all interactions taking place between Mg(2+) and an RNA uses a preferential interaction coefficient, Gamma(2+), which represents the "excess" Mg(2+) neutralizing the RNA charge. The difference between Gamma(2+) for the native and unfolded RNA forms (DeltaGamma(2+)) is the number of Mg(2+) ions "taken up" by an RNA upon folding. Here we determine the conditions under which the Hill coefficient n can be equated to the ion uptake DeltaGamma(2+) and find that two approximations are necessary: (i) the Mg(2+) activity coefficient is independent of concentration during a titration, and (ii) the dependence of DeltaGamma(2+) on Mg(2+) concentration is weak. Titration experiments with a Mg(2+)-binding dye and an adenine-binding riboswitch were designed to test thes...Continue Reading

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Citations

Mar 3, 2011·Biochemistry·Desirae Leipply, David E Draper
Jul 23, 2011·Journal of the American Chemical Society·Desirae Leipply, David E Draper
May 23, 2012·Journal of the American Chemical Society·Ryan L HayesKarissa Y Sanbonmatsu
Jun 19, 2013·Journal of the American Chemical Society·Duncan KilburnSarah A Woodson
Aug 19, 2011·Nature Reviews. Genetics·Yue WanHoward Y Chang
Feb 7, 2012·Proceedings of the National Academy of Sciences of the United States of America·Julie L FioreDavid J Nesbitt
Mar 13, 2014·Annual Review of Biochemistry·Jan LipfertDaniel Herschlag
Jul 27, 2015·Journal of Molecular Biology·Michael J RauKathleen B Hall
Oct 26, 2010·Biochemical and Biophysical Research Communications·Yi-Yong YanZhi-Shu Huang
Apr 8, 2014·Biophysical Journal·Ryan L HayesJosé N Onuchic
May 23, 2015·Electrophoresis·Conny UngerFay Betsou
Jul 17, 2012·Journal of Molecular Biology·Julie L FioreDavid J Nesbitt
Sep 10, 2013·Biophysical Chemistry·Elizabeth J DenningAlexander D MacKerell
Apr 17, 2012·Cell·Reza BehrouziSarah A Woodson
Dec 11, 2013·Physical Chemistry Chemical Physics : PCCP·Zhaojian HeShi-Jie Chen
Dec 30, 2014·Nucleic Acids Research·Hui-Ting LeeSarah A Woodson
Mar 24, 2015·PloS One·Yuhong ZhuShi-Jie Chen
Aug 6, 2016·Proceedings of the National Academy of Sciences of the United States of America·Namita BisariaDaniel Herschlag
Oct 30, 2016·Journal of Molecular Biology·Robb Welty, Kathleen B Hall
Jan 25, 2017·Nucleic Acids Research·Robert J Trachman, David E Draper
Jul 13, 2017·Journal of Nucleic Acids·W-Matthias LeederH Ulrich Göringer
Sep 14, 2018·The Journal of Physical Chemistry Letters·Joon Ho RohSarah A Woodson

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