Biomedical Engineering Reference
In-Depth Information
flexible junctions can lead to large changes in the overall structure of the
molecule, and therefore, its overall alignment [Figure 9.4(B)].
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A domain elongation strategy has been developed to decouple internal and
overall motions in RNA.
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Here, a given helix in a target RNA is elongated,
typically by a stretch of 22 base pairs, in order to dominate the overall shape of
the molecule, and therefore, its overall alignment, in ordering media or when
under the influence of the magnetic field [Figure 9.4(B)]. In this manner,
internal motions occurring elsewhere in the molecule have a small effect on the
overall shape and therefore alignment of the molecule. The elongated helixis
not tagged onto the molecule, where tagging can give rise to complications due
to mobility between the tag and target molecule. Rather, it is rigidly integrated
within the natural framework of the molecule. To minimise resonance
overlap the elongation can be rendered 'NMR invisible' by using an alternating
'GC/CG' elongated helix and A/U labeling or vice versa [Figure 9.4(B)].
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The elongation also has other benefits. To a very good approximation, the
elongated helix can be assumed to have an idealised A-form helical geometry.
This makes it relatively straightforward to determine the overall alignment of
the RNA by using RDCs measured in the elongated helix.
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Protocols have
been developed that allow accurate estimation of any uncertainty in the overall
alignment tensor arising due to A-form structural noise and RDC measure-
Figure 9.4
Dynamic interpretation of RDCs. (A) Molecular frames and rotations used
in the analytical treatment of motions and their impact on RDC
observables. (B) Domain elongation as a strategy for decoupling internal
and overall motions. (C) Flowchart for RDC-directed construction of
RNA dynamic ensembles using the sample and select (SAS) approach.
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