Mapping protein–RNA interactions
Robert Vaughan, William Running, Rongsu Qi, C Cheng Kao
The Biochemistry Interdisciplinary Program, Indiana University, Bloomington, IN, USA
Abstract: There is a significant need to develop approaches for rapid and accurate mapping of protein–ribonucleic acid (RNA) interactions, especially to complement structure-based methods. Approaches using mass spectrometry to map regions in proteins that contact RNA have now been established. These include a reversible crosslinking affinity purification method, residue-specific modification interference assay, and photoactivatable crosslinking and mass spectrometry. Novel methods to identify nucleotides within RNA that contact proteins using photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation are also available. In combination, these methods should generate results that will lead to more specific hypotheses concerning the biological properties of protein–RNA interactions. This review summarizes some recent advances in select assays useful for mapping protein–RNA interactions.
Keywords: hepatitis C virus, positive-strand RNA virus, reversible crosslinking, RNA binding, mass spectrometry
© 2012 The Author(s). This work is published and licensed by Dove Medical Press Limited. The full terms of this license are available at https://www.dovepress.com/terms.php and incorporate the Creative Commons Attribution - Non Commercial (unported, v3.0) License. By accessing the work you hereby accept the Terms. Non-commercial uses of the work are permitted without any further permission from Dove Medical Press Limited, provided the work is properly attributed. For permission for commercial use of this work, please see paragraphs 4.2 and 5 of our Terms.