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PDBsum entry 1zig
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References listed in PDB file
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Key reference
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Title
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A network of heterogeneous hydrogen bonds in gnra tetraloops.
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Authors
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F.M.Jucker,
H.A.Heus,
P.F.Yip,
E.H.Moors,
A.Pardi.
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Ref.
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J Mol Biol, 1996,
264,
968-980.
[DOI no: ]
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PubMed id
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Abstract
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RNA hairpin loops containing a GNRA consensus sequence are the most frequently
occurring hairpins in a variety of prokaryotic and eukaryotic RNAs. These
tetraloops play important functional roles in RNA folding, in RNA-RNA tertiary
interactions and as protein binding sites. Homo and heteronuclear NMR
spectroscopy have been used to determine the structures of the most abundant
members of the GNRA tetraloop family: the GAGA, GCAA and GAAA loops closed by a
C-G base pair. Analysis of the structures of these three hairpin loops reveals a
network of heterogeneous hydrogen bonds. The loops contain a G-A base pair, a G
base-phosphate hydrogen bond and several 2' OH-base hydrogen bonds. These
intramolecular interactions and the extensive base stacking in the loop help
explain the high thermodynamic stability and give insight into the diverse
biological roles of the GNRA RNA hairpins.
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Figure 6.
Figure 6. Schematic drawing of the hydrogen bonding
network proposed for GNRA tetraloops. The following
hydrogen bonds are indicated: G5 H2 to A8 N7, G5 N3
to A8 H6, G5 O2' to A8 H6, G5 2'OH to the six and seven
positions of nucleotide 7, G5 H2 to A8 OP and G5 H1 to
A8 OP.
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Figure 7.
Figure 7. Comparison of the
GCAA and GAGA loops, illustrates
small differences in hydrogen bond-
ing patterns. The hydrogen bonding
between -G5 2'OH and the third
base of the loops are shown. No
hydrogen atoms are displayed ex-
cept the G5 2'OH and the protons of
the third base, which are shown in
dark circles. (a) In the GCAA loop
the 2' hydroxyl group of G5 can
interact with the N7 of A7 and the
amino group of A7. (b) In the
GAGA loop the 2' hydroxyl group
of G5 can interact with the N7 of G7
or with the O6 of G7.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1996,
264,
968-980)
copyright 1996.
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Secondary reference #1
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Title
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Structural features that give rise to the unusual stability of RNA hairpins containing gnra loops.
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Authors
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H.A.Heus,
A.Pardi.
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Ref.
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Science, 1991,
253,
191-194.
[DOI no: ]
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PubMed id
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Headers
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