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PDBsum entry 376d
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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 zipper-Like duplex in DNA: the crystal structure of d(gcgaaagct) at 2.1 a resolution.
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Authors
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W.Shepard,
W.B.Cruse,
R.Fourme,
E.De la fortelle,
T.Prangé.
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Ref.
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Structure, 1998,
6,
849-861.
[DOI no: ]
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PubMed id
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Abstract
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BACKGROUND: The replication origin of the single-stranded (ss)DNA bacteriophage
G4 has been proposed to fold into a hairpin loop containing the sequence
GCGAAAGC. This sequence comprises a purine-rich motif (GAAA), which also occurs
in conserved repetitive sequences of centromeric DNA. ssDNA analogues of these
sequences often show exceptional stability which is associated with hairpin
loops or unusual duplexes, and may be important in DNA replication and
centromere function. Nuclear magnetic resonance (NMR) studies indicate that the
GCGAAAGC sequence forms a hairpin loop in solution, while centromere-like
repeats dimerise into unusual duplexes. The factors stabilising these unusual
secondary structure elements in ssDNA, however, are poorly understood. RESULTS:
The nonamer d(GCGAAAGCT) was crystallised as a bromocytosine derivative in the
presence of cobalt hexammine. The crystal structure, solved by the multiple
wavelength anomalous dispersion (MAD) method at the bromine K-edge, reveals an
unexpected zipper-like motif in the middle of a standard B-DNA duplex. Four
central adenines, flanked by two sheared G.A mismatches, are intercalated and
stacked on top of each other without any interstrand Watson-Crick base pairing.
The cobalt hexammine cation appears to participate only in crystal cohesion.
CONCLUSIONS: The GAAA consensus sequence can dimerise into a stable zipper-like
duplex as well as forming a hairpin loop. The arrangement closes the minor
groove and exposes the intercalated, unpaired, adenines to the solvent and
DNA-binding proteins. Such a motif, which can transform into a hairpin, should
be considered as a structural option in modelling DNA and as a potential binding
site, where it could have a role in DNA replication, nuclease resistance, ssDNA
genome packaging and centromere function.
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Figure 3.
Figure 3. Stereo view of the zipper-like motif. A closeup
view of the central adenine tract cut out from the duplex. The
figure illustrates the substantial buckling of the sheared G·A
mismatch located at the bottom of the figure. Atoms are shown in
standard colours.
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The above figure is
reprinted
by permission from Cell Press:
Structure
(1998,
6,
849-861)
copyright 1998.
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Secondary reference #1
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Title
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Rna tertiary structure mediation by adenosine platforms.
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Authors
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J.H.Cate,
A.R.Gooding,
E.Podell,
K.Zhou,
B.L.Golden,
A.A.Szewczak,
C.E.Kundrot,
T.R.Cech,
J.A.Doudna.
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Ref.
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Science, 1996,
273,
1696-1699.
[DOI no: ]
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PubMed id
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Secondary reference #2
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Title
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Solution structure of a metal-Binding site in the major groove of RNA complexed with cobalt (III) hexammine.
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Authors
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J.S.Kieft,
I.Tinoco.
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Ref.
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Structure, 1997,
5,
713-721.
[DOI no: ]
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PubMed id
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Figure 4.
Figure 4. Stereoview of the average structure of the P5b
stem loop-cobalt (III) hexammine complex. The ligand is located
in the major groove near the two guanines of the G-U base pairs.
The G-U base pairs are shown in yellow, the GAAA tetraloop is
shown in light green, the cobalt (III) hexammine is shown in red
and the rest of the molecule is in blue. Note that the cobalt
(III) hexammine ion is located near the guanine residues, in
position to hydrogen bond to the guanine base carbonyl oxygen
and N7 groups.
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The above figure is
reproduced from the cited reference
with permission from Cell Press
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Secondary reference #3
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Title
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Extraordinary stable structure of short single-Stranded DNA fragments containing a specific base sequence: d(gcgaaagc).
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Authors
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I.Hirao,
Y.Nishimura,
T.Naraoka,
K.Watanabe,
Y.Arata,
K.Miura.
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Ref.
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Nucleic Acids Res, 1989,
17,
2223-2231.
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PubMed id
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Secondary reference #4
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Title
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Structural basis for stabilization of z-Dna by cobalt hexaammine and magnesium cations.
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Authors
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R.V.Gessner,
G.J.Quigley,
A.H.Wang,
G.A.Van der marel,
J.H.Van boom,
A.Rich,
A.Rich.
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Ref.
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Biochemistry, 1985,
24,
237-240.
[DOI no: ]
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PubMed id
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Headers
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