Investigating RNAs Involved in Translational Control by NMR and SAXS - Biophysical Approaches to Translational Control of Gene Expression - page 146

Fig. 8.6 NMR measurements used to study RNA dynamics for motions in the picosecond (ps) to
second (s) timescale. Adapted from Shajani and Varani ( 2007 )
approaches have been developed to probe RNA dynamics: molecular dynamics
simulations (Hall 2008 ; Chen 2008 ; Mackerell and Nilsson 2008 ) , single-molecule
fluorescence spectroscopy (Roy et al. 2008 ; Zhao and Rueda 2009 ; Walter 2001 ) , time-
resolved hydroxyl radical footprinting techniques (Sclavi et al. 1998 ; Shcherbakova
et al. 2006 ), single-molecule force measurements (Li et al. 2008 ) , and NMR meth-
ods (Shajani and Varani 2007 ; Getz et al. 2007 ; Furtig et al. 2007 ; Rinnenthal et al.
2011 ). In this section, we highlight the different approaches for measuring RNA
dynamics using NMR.
NMR provides a unique way to investigate dynamics over time scales encom-
passing biologically relevant motions (Fig. 8.6 ) (Shajani and Varani 2007 ; Getz
et al. 2007 ; Rinnenthal et al. 2011 ). Dynamic motions can occur at the atomic level
or can correspond to entire domains (Getz et al. 2007 ). RNA motions in the picosec-
ond to nanosecond range reflect local motions (Shajani and Varani 2007 ) . These
motions are characterized by measuring the longitudinal ( T 1 ) and transverse ( T 2 )
relaxation rates for 13 C or 15 N nuclei, and the heteronuclear NOE between these
nuclei and their bonded protons. The Lipari-Szabo model free approach (Lipari and
Szabo 1982 ) is the most popular method utilized to quantitatively describe these
motional amplitudes and their rates. These types of experiments have proved very
useful in characterizing local motions for several RNAs (Shajani and Varani 2005 ;
Duchardt and Schwalbe 2005 ; Akke et al. 1997 ; Dayie et al. 2002 ; Musselman et al.
2010 ; Hall and Tang 1998 ). Slower motions in the microsecond to millisecond range
are often reflective of more complex dynamic processes such as conformational
changes, domain motions, folding, and ligand binding. These motions can be inves-
tigated using relaxation dispersion experiments (Shajani and Varani 2005 ; Kloiber
et al. 2011 ; Johnson and Hoogstraten 2008 ). Several examples demonstrating the
use of these techniques to study RNA are available (Duchardt and Schwalbe 2005 ;
Kloiber et al. 2011 ; Blad et al. 2005 ; Dethoff et al. 2008 ). Slow processes on the
millisecond to second timescale can be measured using ZZ-exchange NMR experi-
ments (Latham et al. 2009 ). Rates for processes that occur on even longer timescales