PMID: 7544890Aug 11, 1995Paper

Use of ultra stable UNCG tetraloop hairpins to fold RNA structures: thermodynamic and spectroscopic applications

Nucleic Acids Research
M Molinaro, I Tinoco

Abstract

RNA molecules of > 20 nucleotides have been the focus of numerous recent NMR structural studies. Several investigators have used the UNCG family of hairpins to ensure proper folding. We show that th UUCG hairpin has a minimum requirement of a two base-pair stem. Hairpins with a CG loop closing base pair and an initial 5'CG or 5'GC base pair have a melting temperature approximately 55 degrees C in 10 mM sodium phosphate. The high stability of even such small hairpins suggests that the hairpin can serve as a nucleation site for folding. For high resolution NMR work, the UNCG loop family (UACG in particular) provides excellent spectroscopic markers in one-dimensional exchangeable spectra, in two-dimensional COSY spectra and in NOESY spectra that clearly define it as forming a hairpin. This allows straightforward initiation of chemical shift assignments.

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Citations

Jul 26, 2012·Journal of the American Chemical Society·Marino J E ResendizMarc M Greenberg
Sep 8, 2012·Nature Protocols·Camille J DelebecqueAriel B Lindner
Oct 18, 2007·Nucleic Acids Research·Zhuoyun ZhuangJoan-Emma Shea
Jul 16, 2008·Nucleic Acids Research·Laurie James, Bruno Sargueil
Jan 1, 1997·Annual Review of Biophysics and Biomolecular Structure·P Brion, E Westhof
Oct 17, 2007·Annual Review of Physical Chemistry·Philip C Bevilacqua, Joshua M Blose
Feb 18, 2010·PLoS Biology·Elisabeth M MahenMartha J Fedor
Apr 19, 2011·Biological Chemistry·Ása B BirgisdottirSteinar D Johansen
Dec 17, 2002·Proceedings of the National Academy of Sciences of the United States of America·Luis R ComolliThomas L James
Oct 7, 2009·Proceedings of the National Academy of Sciences of the United States of America·Jonathan F ArambulaSteven C Zimmerman
Jul 2, 2015·Journal of Molecular Recognition : JMR·Emane Y Abdallah, Colin A Smith
Aug 4, 2007·Journal of Molecular Biology·Isabelle LebarsDominique Fourmy
Oct 15, 2013·Wiley Interdisciplinary Reviews. RNA·Roopa ThaparEdward P Nikonowicz
Oct 10, 2009·The EMBO Journal·Nicolás G BolognaJavier F Palatnik
Jun 19, 2008·The Journal of General Virology·Jeremy R ThompsonMark Tepfer
Mar 1, 1997·Nucleic Acids Research·J A BerglundM Rosbash
Feb 18, 2010·Biophysical Journal·Nan-Jie Deng, Piotr Cieplak
Sep 6, 2012·Biochemistry·Breeze N BriggsDavid R McMillin
Oct 2, 2013·The Journal of Physical Chemistry. B·Aaron L Stancik, Eric B Brauns
Dec 30, 2016·Journal of Chemical Theory and Computation·Changwon YangYoungshang Pak
Jan 10, 2017·Physical Chemistry Chemical Physics : PCCP·Aditi N BorkarMichele Vendruscolo
May 30, 2017·Nature Chemical Biology·Robert J TrachmanAdrian R Ferré-D'Amaré
Aug 9, 2019·Nucleic Acids Research·Chaminda D GunawardeneK Andrew White
Jun 17, 2016·RNA·Dhwani N Rupani, Gregory J Connell
Jan 14, 2017·Nucleic Acids Research·Denise Martinez-ZapienAnne-Catherine Dock-Bregeon
Jun 20, 2019·Nucleic Acids Research·Lin HuangDavid M J Lilley

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