Structure folding of RNA kissing complexes in salt solutions: predicting 3D structure, stability, and folding pathway

RNA
Lei JinZhi-Jie Tan

Abstract

RNA kissing complexes are essential for genomic RNA dimerization and regulation of gene expression, and their structures and stability are critical to their biological functions. In this work, we used our previously developed coarse-grained model with an implicit structure-based electrostatic potential to predict three-dimensional (3D) structures and stability of RNA kissing complexes in salt solutions. For extensive RNA kissing complexes, our model shows great reliability in predicting 3D structures from their sequences, and our additional predictions indicate that the model can capture the dependence of 3D structures of RNA kissing complexes on monovalent/divalent ion concentrations. Moreover, the comparisons with extensive experimental data show that the model can make reliable predictions on the stability for various RNA kissing complexes over wide ranges of monovalent/divalent ion concentrations. Notably, for RNA kissing complexes, our further analyses show the important contribution of coaxial stacking to the 3D structures and stronger stability than the corresponding kissing-interface duplexes at high salts. Furthermore, our comprehensive analyses for RNA kissing complexes reveal that the thermally folding pathway for a ...Continue Reading

References

Sep 27, 1994·Proceedings of the National Academy of Sciences of the United States of America·A E WalterM Zuker
May 19, 1995·Journal of Molecular Biology·R S Gregorian, D M Crothers
Jun 9, 1995·Science·J P MarinoD M Crothers
May 28, 1996·Proceedings of the National Academy of Sciences of the United States of America·J C PaillartR Marquet
Jun 17, 1998·Nature Structural Biology·A MujeebT G Parslow
Aug 10, 2000·Proceedings of the National Academy of Sciences of the United States of America·C H Kim, I Tinoco
Jun 28, 2001·Proceedings of the National Academy of Sciences of the United States of America·A A Andersen, R A Collins
Aug 14, 2002·Biochemistry·Hendrik Huthoff, Ben Berkhout
Oct 5, 2002·Nucleic Acids Research·Sébastien Lemieux, François Major
Jun 26, 2003·Nucleic Acids Research·Michael Zuker
Jun 26, 2003·Nucleic Acids Research·Huanwang YangEric Westhof
Jul 9, 2004·Biophysical Journal·Roumen A Dimitrov, Michael Zuker
Sep 24, 2004·RNA·Marc RehmsmeierRobert Giegerich
Oct 2, 2004·Nucleic Acids Research·Albert WeixlbaumerRenée Schroeder
Jan 13, 2005·Journal of Molecular Biology·Mirela AndronescuAnne Condon
Apr 7, 2005·Current Opinion in Chemical Biology·Sarah A Woodson
May 5, 2005·Annual Review of Biophysics and Biomolecular Structure·David E DraperAna Maria Soto
Nov 23, 2005·RNA·Nicolas PiganeauRenée Schroeder
Jan 18, 2006·Nucleic Acids Research·Christina LorenzRenée Schroeder
Jan 18, 2006·Nucleic Acids Research·Fabien KiekenGérard Lancelot
May 18, 2006·Annual Review of Phytopathology·W Allen Miller, K Andrew White
Dec 6, 2006·Nucleic Acids Research·Zhi-Jie Tan, Shi-Jie Chen
Feb 14, 2007·Journal of the American Chemical Society·Eda KoculiSarah A Woodson
Feb 27, 2007·Journal of the American Chemical Society·Victor K TamYitzhak Tor
Feb 28, 2007·Biophysical Journal·Zhi-Jie Tan, Shi-Jie Chen
Mar 27, 2007·Current Opinion in Structural Biology·Bruce A ShapiroEckart Bindewald
Aug 30, 2007·Proceedings of the National Academy of Sciences of the United States of America·Rhiju Das, David Baker
Sep 5, 2007·Nucleic Acids Research·Isabelle LebarsJean-Jacques Toulmé
Mar 7, 2008·Nature·Marc Parisien, François Major
Apr 11, 2008·Journal of Biomolecular Structure & Dynamics·Hugo M MartinezBruce A Shapiro
Jun 25, 2008·Annual Review of Biophysics·Shi-Jie Chen
Jul 9, 2008·Proceedings of the National Academy of Sciences of the United States of America·Hélène Van MelckebekeJérôme Boisbouvier

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Citations

Nov 5, 2019·The Journal of Chemical Physics·Ben-Gong ZhangYa-Zhou Shi
Oct 21, 2020·Physical Review. E·Qiangqiang DuanYi Xiao
May 1, 2021·Frontiers in Molecular Biosciences·Chenjie FengZhi-Jie Tan

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