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Review
. 2008 Dec;12(6):612-8.
doi: 10.1016/j.cbpa.2008.09.033. Epub 2008 Oct 26.

RNA in motion

Kathleen B Hall  1
Affiliations
Review

RNA in motion

Kathleen B Hall. Curr Opin Chem Biol. 2008 Dec.

Abstract

Although RNA duplex regions are highly structured and inflexible, other elements of an RNA molecule are capable of dynamic motions. These flexible regions are the sites of interactions with small molecules, proteins, and other RNAs, yet there are few descriptions of these regions that include the timescale and amplitude of their motions. No one technique is sufficient to accurately describe these motions, but the combination of in vitro methods, particularly NMR relaxation methods, and more robust in silico methods, is beginning to yield the type of data that can be used to understand RNA function. Very few RNAs have been described by both techniques, and here one such RNA and one RNA:protein complex are reviewed.

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Figures

Figure 1
Figure 1
Dynamic RNAs. The secondary structures of those RNAs for which both in vitro and in silico dynamics data are available. TAR RNA: NMR ref –; MD: ref . IRE RNA hairpin: NMR ref , ; MD: 26. L11/GTPase Associated Center RNA. The upper stem is Helix 43, and the bottom stem is Helix 44. MD ref ,. UUCG/CAGC tetraloops: NMR/MD ref ; MD 5,7. TAR is Transactivation response element; IRE is Iron Response Element.
Figure 2
Figure 2
The canonical UUCG loop structure. A tertiary structure of the U1U2C3G4 tetraloop. The U1:G4 bases are hydrogen bonding, U2 extends into solution with no interactions, and C3 stacks over the U:G base interaction. Image made with VMD (29).
Figure 3
Figure 3
An NMR structure of the free B stearothermophilus L11 protein. Those regions of the protein that have significant dynamical motions (ps-ns) in the free form are labeled. Backbone dynamics of the protein were measured by NMR relaxation measurements (9). Image made with VMD (29).
Figure 4
Figure 4
Structures of the L11:GAC complex. Different orientations of the N-terminal domain of L11 protein in the complex with GAC RNA seen in NMR and crystal structures. NMR structure: pdb 2jq7 (9). X-ray crystal structure of the L11/CAG complex: pdb 1mms (13). X-ray crystal structure of the ribosome: pdb 1qa4 (28). Image made with VMD (29).
Figure 5
Figure 5
The tertiary fold of a GAC. This crystal structure of the E coli GAC was taken from a structure of the L11:GAC complex (27). The flexible A1067 is shown in yellow. A1067 is one of a very few nucleotides that shows dynamic motions in simulations. Image made with VMD (29).
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References

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