Investigating RNAs Involved in Translational Control by NMR and SAXS - Biophysical Approaches to Translational Control of Gene Expression - page 156

Fig. 8.12 NMR and SAXS refinement of an RNA:RNA complex. Comparison of the ab initio
structure ( gray spheres ) with the NMR structure of the complex refined in the absence ( red ) and
presence ( blue ) of SAXS restraints. Inclusion of SAXS restraints results in better agreement with
measured R g (Zuo et al. 2008 ) and a better fit with the ab initio structure (unpublished data)

8.2 Using NMR and SAXS to Study RNAs Involved

in Translational Control

RNA structural elements, such as internal ribosomal entry sites (IRESs) (Balvay
et al. 2009 ) and programmed ribosomal frameshift sites (PRFS) (Brierley 1995 ;
Farabaugh 1996 ), are widely used in biology to regulate translation. IRESs facilitate
cap-independent translation (Balvay et al. 2009 ; Shatsky et al. 2010 ) , range in size
from 250 to 500 nucleotides, and are typically composed of several stable domains,
including stem-loops and pseudoknots. PRFS, which increase genomic coding
capacity by promoting a change in reading frame during translation, are composed
of three essential elements: a heptanucleotide “slippery” sequence, a linker region,
and a downstream RNA structure, such as a pseudoknot or stem-loop (Giedroc and
Cornish 2009 ). While biochemical and genetic results highlight the functional
importance of IRESs and PRFS, structural information is needed to understand the
roles of structure and dynamics in the function of these RNAs. The following sec-
tions highlight several examples of RNAs involved in translation control that have
been characterized using NMR and SAXS.

8.2.1 Programmed Ribosomal Frameshift Sites

NMR has been employed to investigate the downstream RNA structures of numer-
ous frameshift sites (Marcheschi et al. 2007, 2009 ; Staple and Butcher 2005a ; Wang