Investigating RNAs Involved in Translational Control by NMR and SAXS - Biophysical Approaches to Translational Control of Gene Expression - page 137

Chapter 8
Investigating RNAs Involved in Translational
Control by NMR and SAXS

Kathryn D. Mouzakis , Jordan E. Burke, and Samuel E. Butcher

8.1 Introduction

Translational control, broadly defined, is the posttranscriptional regulation of gene
expression within a cell. The majority of translational control is thought to rely on
the interaction of regulatory proteins with messenger RNA (mRNA) (Keene 2007 ) .
However, a growing body of evidence indicates that mRNA structures play an
important role in translational control. For example, certain classes of riboswitches
form dynamic RNA structures that influence translation (Lemay et al. 2011 ) .
Additionally, RNA-RNA interactions can broadly control translation, as in the case
of microRNA (Bartel 2009 ). Therefore, it is important to consider the role of RNA
structure and intrinsic dynamic motions that can modulate RNA function during
translation (Talini et al. 2011 ; Bailor et al. 2010 ) .
Historically, the most informative structural information related to RNA struc-
ture and its role in translation has been derived from X-ray crystallography, with the
most striking example of this being the structure of the ribosome (Yusupov et al.
2001 ; Ban et al. 2000 ; Carter et al. 2000 ; Selmer et al. 2006 ; Gluehmann et al. 2001 ;
Pioletti et al. 2001 ; Zhao 2011 ). However, obtaining diffraction quality crystals of
RNA can be tremendously challenging. Alternatives to X-ray crystallography are
nuclear magnetic resonance (NMR) and small angle X-ray scattering (SAXS),
which are solution-based methods. In addition to providing structural information,
NMR can be used to investigate dynamic motions. In this chapter, we review meth-
ods for investigating RNA structure and dynamics in solution. In Sect. 8.1 , we focus
predominately on NMR spectroscopy and SAXS as complementary techniques for
analyzing RNA structure and dynamics in solution. In Sect. 8.2 , speci fi c examples
of RNAs involved in translational control are discussed.

K. D. Mouzakis • J. E. Burke • S. E. Butcher ( * )
Department of Biochemistry , University of Wisconsin ,
Madison , WI , USA
email: [e-mail]