Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Comparative Study
. 2000 Nov 1;28(21):4376-81.
doi: 10.1093/nar/28.21.4376.

Synthesis and crystal structure of an octamer RNA r(guguuuac)/r(guaggcac) with G.G/U.U tandem wobble base pairs: comparison with other tandem G.U pairs

J Deng  1 , M Sundaralingam
Affiliations
Comparative Study

Synthesis and crystal structure of an octamer RNA r(guguuuac)/r(guaggcac) with G.G/U.U tandem wobble base pairs: comparison with other tandem G.U pairs

J Deng et al. Nucleic Acids Res. .

Abstract

We have determined the crystal structure of the RNA octamer duplex r(guguuuac)/r(guaggcac) with a tandem wobble pair, G.G/U.U (motif III), to compare it with U.G/G.U (motif I) and G.U/U.G (motif II) and to better understand their relative stabilities. The crystal belongs to the rhombohedral space group R3. The hexagonal unit cell dimensions are a = b = 41.92 A, c = 56.41 A, and gamma = 120 degrees, with one duplex in the asymmetric unit. The structure was solved by the molecular replacement method at 1.9 A resolution and refined to a final R: factor of 19.9% and R(free) of 23.3% for 2862 reflections in the resolution range 10.0-1.9 A with F >/= 2sigma(F). The final model contains 335 atoms for the RNA duplex and 30 water molecules. The A-RNA stacks in the familiar head-to-tail fashion forming a pseudo-continuous helix. The uridine bases of the tandem U.G pairs have slipped towards the minor groove relative to the guanine bases and the uridine O2 atoms form bifurcated hydrogen bonds with the N1 and N2 of guanines. The N2 of guanine and O2 of uridine do not bridge the 'locked' water molecule in the minor groove, as in motifs I and II, but are bridged by water molecules in the major groove. A comparison of base stacking stabilities of motif III with motifs I and II confirms the result of thermodynamic studies, motif I > motif III > motif II.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Schematic representations of base pairings of the three tandem G·U pairs: (a) motif I with the sequence r(guaugua)dC; (b) motif II with the sequence r(gugugua)dC; (c) motif III with the sequence r(guguuuac)/r(guaggcac).
Figure 2
Figure 2
Hydration network of the G·U wobble pairs; the water molecules are labeled. Note that the major grooves are hydrated. (a) The first G·U wobble pair; (b) the second G·U pair.
Figure 3
Figure 3
(a) Close view of the O2′–O4′ interaction between residues U4 and U5. (b) The intramolecular hydrogen bonds between O2′ hydroxyl groups and O4′ sugar ring atoms in motif III are shown by broken red lines.
Figure 4
Figure 4
(a) View of the crystal packing in the hexagonal unit cell down the c-axis. (b) View of the crystal packing in the unit cell perpendicular to the c-axis.
Figure 5
Figure 5
Base pair stacking in motifs I (a–c), II (d–f) and III (g–i). All the G·U wobbles are shown in green and all the flanking Watson–Crick pairs are yellow. (a) Stacking of the first G·U wobble with its 5′ flanking Watson–Crick pair with a twist angle of 26.7°. (b) Stacking of the tandem G·U wobbles with a high twist angle of 38.1°. (c) Stacking of the second G·U wobble with its 3′ flanking Watson–Crick pair with a low twist angle of 26.3°. (d) Stacking of the first G·U wobble with its 5′ flanking Watson–Crick pair with a twist angle of 30°. (e) Stacking of the tandem G·U wobbles with a low twist angle of 24°. (f) Stacking of the second G·U wobble with its 3′ flanking Watson–Crick pair with a high twist angle of 34°. (g) Stacking of the U4·G13 wobble pair with its 5′ flanking Watson–Crick pair with a twist angle of 33.93°. (h) Stacking of the tandem wobble pairs in motif III, U·U/G·G, with a twist angle of 32.20°. (i) Stacking of the 3′ side G·U wobble with its 3′ flanking Watson–Crick pair with a high twist angle of 37.23°.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Modrich P. (1987) Annu. Rev. Biochem., 56, 435. - PubMed
    1. Pearl L.H. and Savva,R. (1995) Trends Biochem. Sci., 20, 421. - PubMed
    1. Varani G. and Pardi,A. (1994) In Nagai,K. and Mattaj,I.W. (eds), RNA–Protein Interactions. Oxford University Press, Oxford, UK, pp. 1–24.
    1. Varani G., Wimberly,B.and Tinoco,I.,Jr (1989) Biochemistry, 28, 7760. - PubMed
    1. Wimberly B., Varani,G. and Tinoco,I.,Jr (1993) Biochemistry, 32, 1078. - PubMed

Publication types