NMR studies of the structure and Mg2+ binding properties of a conserved RNA motif of EMCV picornavirus IRES element

Nucleic Acids Research
Marie M PhelanVasudevan Ramesh

Abstract

The structure and Mg(2+) binding properties of a conserved 75mer RNA motif of the internal ribosome entry site (IRES) element of encephalomyocarditis virus picornavirus have been investigated by (1)H-NMR and UV melting experiments. The assignment of the imino proton resonances with characteristic chemical shift dispersion for canonical and non-canonical base pairs confirmed the predicted secondary structure of the 75mer and its fragments. Addition of Mg(2+) resulted in a dramatic increase in apparent melting temperature, with the 75mer RNA registering the biggest increase, from 63 to 80 degrees C, thus providing evidence for enhanced stability arising from Mg(2+) binding. Similarly, addition of Mg(2+) induced selective changes to the chemical shifts of the imino protons of a GCGA tetraloop in the 75mer, that is essential for IRES activity, thereby highlighting a possible structural role for Mg(2+) in the folding of the 75mer. Significantly, the same protons show retarded exchange to water solvent, even at elevated temperature, which suggest that Mg(2+) induces a conformational rearrangement of the 75mer. Thus, we propose that Mg(2+) serves two important roles: (i) enhancing thermodynamic stability of the 75mer RNA (and its subm...Continue Reading

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Citations

Aug 12, 2009·Journal of Biological Physics·J A Dupont, K Snoussi
Jul 12, 2011·Nucleic Acids Research·Noemí FernándezEncarnación Martínez-Salas
Apr 27, 2012·Comparative and Functional Genomics·Encarnación Martínez-SalasNoemí Fernández
Jan 19, 2016·Journal of Molecular Biology·Gloria LozanoEncarnacion Martinez-Salas
Nov 8, 2015·Biochemical and Biophysical Research Communications·Sandra Aurora Telpalo-CarpioJosé Manuel Aguilar-Yáñez
Jun 17, 2008·Biophysical Chemistry·Jörg C Schlatterer, Nancy L Greenbaum
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Nov 9, 2010·Virology·Noemí FernándezEncarnación Martínez-Salas
Aug 12, 2008·Virus Research·Olga Fernández-MiragallEncarnación Martínez-Salas
Feb 15, 2008·The Journal of General Virology·Encarnación Martínez-SalasNoemi Fernandez
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Oct 25, 2012·Chemical Communications : Chem Comm·Kwong Kit Chan, Vasudevan Ramesh
Oct 20, 2007·The Journal of General Virology·Olga Fernández-Miragall, Encarnación Martínez-Salas

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