Electrostatic free energy landscapes for DNA helix bending

Biophysical Journal
Zhi-Jie Tan, Shi-Jie Chen

Abstract

Nucleic acids are highly charged polyanionic molecules; thus, the ionic conditions are crucial for nucleic acid structural changes such as bending. We use the tightly bound ion theory, which explicitly accounts for the correlation and ensemble effects for counterions, to calculate the electrostatic free energy landscapes for DNA helix bending. The electrostatic free energy landscapes show that DNA bending energy is strongly dependent on ion concentration, valency, and size. In a Na(+) solution, DNA bending is electrostatically unfavorable because of the strong charge repulsion on backbone. With the increase of the Na(+) concentration, the electrostatic bending repulsion is reduced and thus the bending becomes less unfavorable. In contrast, in an Mg(2+) solution, ion correlation induces a possible attractive force between the different parts of the helical strands, resulting in bending. The electrostatically most favorable and unfavorable bending directions are toward the major and minor grooves, respectively. Decreasing the size of the divalent ions enhances the electrostatic bending attraction, causing an increased bending angle, and shifts the most favorable bending to the direction toward the minor groove. The microscopic an...Continue Reading

References

Apr 1, 1989·Journal of Biomolecular Structure & Dynamics·G S ManningA Rich
May 1, 1989·Biopolymers·B JayaramB Honig
Dec 1, 1986·Journal of Biomolecular Structure & Dynamics·D Porschke
Jan 1, 1988·Annual Review of Biophysics and Biophysical Chemistry·P J Hagerman
Jun 28, 1972·Biochemical and Biophysical Research Communications·S Arnott, D W Hukins
Oct 11, 1984·Nature·T J RichmondA Klug
Oct 1, 1981·Biopolymers·V Rizzo, J Schellman
Jan 1, 1995·Annual Review of Physical Chemistry·C F Anderson, M T Record
Dec 16, 1994·Science·J K Strauss, L J Maher
May 6, 1994·Journal of Molecular Biology·J AntosiewiczM K Gilson
Sep 3, 1996·Proceedings of the National Academy of Sciences of the United States of America·J K StraussL J Maher
Jun 10, 1997·Proceedings of the National Academy of Sciences of the United States of America·C G BaumannC Bustamante
Jan 1, 1997·Biopolymers·V A Bloomfield
Jun 23, 1998·Biophysical Journal·I Rouzina, V A Bloomfield
Jan 23, 1999·Current Opinion in Chemical Biology·L J Maher
Aug 15, 2000·Annual Review of Biophysics and Biomolecular Structure·L D Williams, L J Maher
Jun 19, 2001·Current Opinion in Structural Biology·N V Hud, M Polak
Aug 23, 2001·Proceedings of the National Academy of Sciences of the United States of America·N A BakerJ A McCammon
Apr 23, 2002·Protein Science : a Publication of the Protein Society·Kelly K LeeBertrand García-Moreno E
Apr 25, 2002·Journal of the American Chemical Society·Konstantin M KosikovGerald S Manning
May 23, 2002·Biophysical Journal·Jay R WennerVictor A Bloomfield
Jul 13, 2002·Biopolymers·Y LuN C Stellwagen
Aug 31, 2002·Journal of Biological Inorganic Chemistry : JBIC : a Publication of the Society of Biological Inorganic Chemistry·Anna Marie Pyle
Feb 15, 2003·Proceedings of the National Academy of Sciences of the United States of America·Andrej BarbicDonald M Crothers
Apr 30, 2003·Biopolymers·Nicholas V Hud, Janez Plavec
Sep 23, 2003·Protein Science : a Publication of the Protein Society·David SeptJ Andrew McCammon
Nov 18, 2003·Proceedings of the National Academy of Sciences of the United States of America·Hugh Nymeyer, Angel E García
Aug 18, 2004·Journal of Molecular Biology·Vladimir TchernaenkoLeonard C Lutter
Nov 24, 2004·Biophysical Journal·Yongjun LuNancy C Stellwagen
Mar 3, 2005·The Journal of Chemical Physics·Zhi-Jie Tan, Shi-Jie Chen
Mar 3, 2005·Nucleic Acids Research·Kevin RangeDarrin M York
Mar 30, 2005·Biochemistry·D Thirumalai, Changbong Hyeon
Apr 7, 2005·Current Opinion in Chemical Biology·Sarah A Woodson
Apr 20, 2005·Current Opinion in Structural Biology·Nathan A Baker
May 5, 2005·Annual Review of Biophysics and Biomolecular Structure·David E DraperAna Maria Soto

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Citations

Dec 12, 2012·Quarterly Reviews of Biophysics·Pengyu RenNathan A Baker
Nov 10, 2011·Physical Biology·Gengsheng Chen, Shi-Jie Chen
Apr 3, 2012·The Journal of Chemical Physics·Melanie J Zimmer, Tihamér Geyer
Apr 5, 2011·The Journal of Chemical Physics·B Eslami-Mossallam, M R Ejtehadi
Aug 12, 2014·The Journal of Chemical Physics·Yuhong Zhu, Shi-Jie Chen
Jan 21, 2010·Biophysical Journal·Gengsheng ChenShi-Jie Chen
Apr 22, 2008·Biophysical Journal·Zhi-Jie Tan, Shi-Jie Chen
Apr 4, 2015·The Journal of Chemical Physics·Yuan-Yan WuZhi-Jie Tan
Sep 6, 2012·Biophysical Journal·Zhi-Jie Tan, Shi-Jie Chen
Sep 8, 2010·Biophysical Journal·Zhi-Jie Tan, Shi-Jie Chen
Jul 5, 2011·Biophysical Journal·Zhi-Jie Tan, Shi-Jie Chen
Mar 24, 2015·PloS One·Yuhong ZhuShi-Jie Chen
Aug 5, 2016·The Journal of Physical Chemistry. B·Tao YuShi-Jie Chen
Dec 11, 2013·Physical Chemistry Chemical Physics : PCCP·Zhaojian HeShi-Jie Chen
Aug 10, 2017·The Journal of Chemical Physics·Xi ZhangZhi-Jie Tan
May 16, 2018·Physical Review. E·A V ZampetakiP Schmelcher
Aug 27, 2014·The Journal of Physical Chemistry. B·Maryna TaranovaIoan Andricioaei

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