Biomedical Engineering Reference
In-Depth Information
lead compound discovery and optimisation.
7,13-15
Experimental data that
probes deeply into dynamic aspects of RNA structure at atomic resolution
over extended timescales is also required to guide developments in computa-
tional force fields, which remain severely underdeveloped for nucleic acids.
16,17
Among several NMR techniques that have been developed and applied to
study RNA dynamics,
6,8,18,19
the measurement of residual dipolar couplings
(RDCs) in partially aligned systems
20-23
is providing new insights into
previously poorly understood aspects of RNA dynamics behavior. There are
several factors that make RDCs attractive probes of RNA dynamics. First,
RDCs can be measured in great abundance between nuclei in base, sugar and
backbone moieties without some of the complications that plague measure-
ments of NMR spin relaxation and relaxation dispersion data. Second, the
timescale sensitivity of RDCs to internal motions extends from picoseconds to
milliseconds and uniquely allows insights into dynamics occurring at
nanosecond to microsecond timescales that are difficult to access by NMR
spin-relaxation methods. Finally, by changing the alignment properties of a
target RNA molecule, more than one RDC data set can be measured,
24,25
providing the basis for mapping out complex 3D motional choreographies
with high spatial resolution.
26-29
Although RDCs continue to be used
primarily as a rich source of long-range orientational constraints for improving
the quality of structures determined by solution-state NMR,
30-33
a growing
number of studies are exploiting the unique dynamics sensitivity of
RDCs,
6,18,23
Here, we review NMR RDC methods for studying RNA
dynamics and highlight some of the new insights that have been obtained.
9.2 Residual Dipolar Coupling Theory
The theoretical underpinnings of dipolar and other anisotropic interactions
have been reviewed extensively both in the context of early liquid-crystal
applications
34-44
and biomolecular applications.
32,45-50
Here we briefly review
the basic theory underpinning RDCs with a specific emphasis on nucleic acid
dynamics applications.
9.2.1 The Dipolar Interaction
Analogous to a pair of bar magnets, nuclear dipole-dipole interactions
originate from the through-space magnetic interaction between two nuclei,
where the local magnetic field at a given nucleus is perturbed by the magnetic
field of a neighboring nucleus. Consider how the dipolar interaction between a
carbon and proton nucleus in a C-H bond modulates the effective magnetic
field at the carbon nucleus [Figure 9.1(A)]. The carbon nucleus experiences the
sum of the static external magnetic field and the much smaller (y10
24
)
magnetic field generated by the proton nucleus. Because the nuclear bar
magnets are always quantised parallel (or anti-parallel) to the magnetic field,
the proton-induced magnetic field experienced by the carbon nucleus will vary
