Abstract
Surface plasmon resonance (SPR)-based instruments have become gold-standard tools for investigating molecular interactions involving macromolecules. The major advantage is that the measured signal is sensitive to changes in mass. Therefore, all kinds of complexes can be analyzed including those with compounds as small as cations. SPR is mainly used to determine the dissociation equilibrium constant and the binding rates of a reaction if slow enough. SPR is well suited for analysis molecular interactions with nucleic acids because these negatively charged macromolecules do not have a tendency to stick to the sensor chip surface as some proteins can do. To illustrate the use of SPR with RNA molecules, we describe methods that we used for monitoring the interaction between the protein Rop from E. coli and two RNA-RNA loop-loop complexes. One is derived from the natural target of Rop, RNAI-RNAII. The other one is an RNA-RNA complex formed between a shortened version of the TAR element of HIV-1 and a structured RNA, TAR* rationally designed to interact with TAR through loop-loop interactions. These methods can be easily adapted to other complexes involving RNA molecules and to other SPR instruments.
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Acknowledgments
We thank the structural biophysico-chemistry facility (UMS 3030/US001 CNRS/Inserm) of the IECB (Pessac, France) for access to the Biacore 3000 instrument and Lætitia Minder, assistant engineer in charge of the SPR facility of the institute, for technical assistance. The SPR instrument was acquired with the support of the “Conseil Régional Nouvelle Aquitaine” (former Région Aquitaine).
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Di Primo, C. (2020). Surface Plasmon Resonance for Investigating Molecular Interactions with RNA. In: Arluison, V., Wien, F. (eds) RNA Spectroscopy. Methods in Molecular Biology, vol 2113. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0278-2_6
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DOI: https://doi.org/10.1007/978-1-0716-0278-2_6
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