A model system for investigating lineshape/structure correlations in RNA site-directed spin labeling

Biochemical and Biophysical Research Communications
Peter Z QinArisa Oki

Abstract

In RNA site-directed spin labeling (SDSL) studies, structural and dynamic information at the individual RNA nucleotide level is derived from the observed electron paramagnetic resonance spectrum of a covalently attached nitroxide. A systematic approach for RNA SDSL is to establish a library that categorizes observed spectral lineshapes based on known RNA structures, thus enabling lineshape-based structure identification at any RNA site. To establish the first RNA SDSL library, selective secondary structure elements have been systematically engineered into a model RNA. Nitroxide lineshapes reporting features specific to each element were obtained utilizing a new avidin-tethering scheme for suppressing spectral effects due to uniform RNA tumbling. The data demonstrated two key features required for a SDSL library with a predicting power: (i) spectral divergence--distinctive lineshape for different elements; and (ii) spectral convergence--similar lineshape for the same element in different contexts. This sets the foundation for further RNA SDSL library development.

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Citations

Feb 18, 2009·Journal of the American Chemical Society·Gian Paola G GrantPeter Z Qin
May 23, 2007·Nucleic Acids Research·Gian Paola G Grant, Peter Z Qin
Apr 30, 2008·Biochemical and Biophysical Research Communications·Gian Paola G GrantPeter Z Qin
Nov 17, 2010·Protein Science : a Publication of the Protein Society·Natasha L PirmanGail E Fanucci
May 29, 2007·Biophysical Journal·Qi CaiPeter Z Qin
Feb 17, 2018·Chemistry : a European Journal·Nilesh R Kamble, Snorri Th Sigurdsson
Jun 17, 2020·Angewandte Chemie·Martin Poncelet, Benoit Driesschaert
Jul 29, 2020·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Karolina BartosikGrazyna Leszczynska
Jan 17, 2009·The Journal of Physical Chemistry. B·Luis GalianoGail E Fanucci

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