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PDBsum entry 1ixj
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DOI no:
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Nucleic Acids Res
30:5253-5260
(2002)
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PubMed id:
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Crystal structure of d(GCGAAAGCT) containing a parallel-stranded duplex with homo base pairs and an anti-parallel duplex with Watson-Crick base pairs.
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T.Sunami,
J.Kondo,
T.Kobuna,
I.Hirao,
K.Watanabe,
K.Miura,
A.Takénaka.
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ABSTRACT
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A DNA fragment d(GCGAAAGCT), known to adopt a stable mini-hairpin structure in
solution, has been crystallized in the space group I4(1)22 with the unit-cell
dimensions a = b = 53.4 A and c = 54.0 A, and the crystal structure has been
determined at 2.5 A resolution. The four nucleotide residues CGAA of the first
half of the oligomer form a parallel duplex with another half through the homo
base pairs, C2:C2+ (singly-protonated between the Watson- Crick sites), G3:G3
(between the minor groove sites), A4:A4 (between the major groove sites) and
A5:A5 (between the Watson-Crick sites). The two strands remaining in the half of
the parallel duplex are split away in different directions, and they pair in an
anti-parallel B-form duplex with the second half extending from a neighboring
parallel duplex, so that an infinite column is formed in a head-to-tail fashion
along the c-axis. It seems that a hexa-ammine cobalt cation supports such a
branched and bent conformation of the oligomer. One end of the parallel duplex
is stacked on the corresponding end of the adjacent parallel duplex; between
them, the guanine base of the first residue is stacked on the fourth ribose of
another duplex.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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E.Ennifar,
S.Bernacchi,
P.Wolff,
and
P.Dumas
(2007).
Influence of C-5 halogenation of uridines on hairpin versus duplex RNA folding.
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RNA,
13,
1445-1452.
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J.Kondo,
T.Sunami,
and
A.Takénaka
(2007).
The structure of a d(gcGAACgc) duplex containing two consecutive bulged A residues in both strands suggests a molecular switch.
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Acta Crystallogr D Biol Crystallogr,
63,
673-681.
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PDB code:
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J.Kondo,
W.Adachi,
S.Umeda,
T.Sunami,
and
A.Takénaka
(2004).
Crystal structures of a DNA octaplex with I-motif of G-quartets and its splitting into two quadruplexes suggest a folding mechanism of eight tandem repeats.
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Nucleic Acids Res,
32,
2541-2549.
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PDB codes:
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M.Egli
(2004).
"Deoxyribo nanonucleic acid"; antiparallel, parallel, and unparalleled.
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Chem Biol,
11,
1027-1029.
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M.Egli
(2004).
Nucleic acid crystallography: current progress.
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Curr Opin Chem Biol,
8,
580-591.
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P.Auffinger,
F.A.Hays,
E.Westhof,
and
P.S.Ho
(2004).
Halogen bonds in biological molecules.
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Proc Natl Acad Sci U S A,
101,
16789-16794.
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P.J.Paukstelis,
J.Nowakowski,
J.J.Birktoft,
and
N.C.Seeman
(2004).
Crystal structure of a continuous three-dimensional DNA lattice.
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Chem Biol,
11,
1119-1126.
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PDB code:
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T.Sunami,
J.Kondo,
I.Hirao,
K.Watanabe,
K.Miura,
and
A.Takénaka
(2004).
Structures of d(GCGAAGC) and d(GCGAAAGC) (tetragonal form): a switching of partners of the sheared G.A pairs to form a functional G.AxA.G crossing.
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Acta Crystallogr D Biol Crystallogr,
60,
422-431.
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PDB codes:
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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