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PDBsum entry 160d
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J Mol Biol
231:431-444
(1993)
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PubMed id:
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High resolution crystal structure of the A-DNA decamer d(CCCGGCCGGG). Novel intermolecular base-paired G*(G.C) triplets.
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B.Ramakrishnan,
M.Sundaralingam.
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ABSTRACT
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The DNA decamer d(CCCGGCCGGG) crystallizes in the orthorhombic space group
P2(1)2(1)2(1) with a = 24.88, b = 44.60 and c = 46.97 A containing a duplex in
the asymmetric unit. The structure was solved by molecular replacement and
refined to an R factor of 18.5% using 6033 reflections at 1.65 A resolution. The
decamer duplex adopts an A-DNA conformation. The abrupt dislocation of the
duplex at the fourth base-pair G(4).C(17) by an abutting symmetry related
molecule results in distortion of the backbone bonds of the fifth residue G(5),
P-O(5')(alpha) and C(4')-C(5')(gamma), to the trans conformations from their
favored gauche- and gauche+ conformations, respectively. In this close encounter
the terminal G(10).C(11) base-pair of the symmetry related molecule hydrogen
bonds to the G(4).C(17) base-pair forming a novel base-paired G(4)*(G10).C(11))
triplet, where G(4) is hydrogen bonded to both G(10) and C(11). To facilitate
this hydrogen bonding the G(4).C(17) base-pair slides into the minor groove,
causing a toll on the backbone conformation of the adjacent residue G(5). A
similar triplet base-pairing interaction with somewhat weaker hydrogen bonds
occurs at the pseudo dyad related C(7).G(14) base-pair with G(20) of another
symmetry related duplex. This pseudo triplet interaction (C(7).G(14))*G(20),
does not perturb the backgone alpha and gamma torsions of G(15). Both the novel
base triplets are non-planar. The abrupt dislocation/bend at the G(4).C(17)
base-pair jolts the global helical base-pair parameters, inclination, tilt,
roll, tip, etc. quite markedly. Therefore a better description of the helix
parameters is obtained by splitting the duplex and calculating the local helix
axis for the top half consisting of the first three base-pairs, and the lower
half consisting of the last six base-pairs, omitting the fourth base-pair. The
two half duplexes are bent by only 10 degrees. This structure further
demonstrates that crystal packing interactions, which can also be governed by
base sequence, play a dominant role in determining DNA conformation.
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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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J.Farwer,
M.J.Packer,
and
C.A.Hunter
(2006).
Prediction of atomic structure from sequence for double helical DNA oligomers.
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Biopolymers,
81,
51-61.
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G.Savitha,
and
M.A.Viswamitra
(1999).
An A-DNA structure with two independent duplexes in the asymmetric unit.
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Acta Crystallogr D Biol Crystallogr,
55,
1136-1143.
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PDB code:
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Y.G.Gao,
H.Robinson,
and
A.H.Wang
(1999).
High-resolution A-DNA crystal structures of d(AGGGGCCCCT). An A-DNA model of poly(dG) x poly(dC).
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Eur J Biochem,
261,
413-420.
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PDB codes:
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B.Schneider,
K.Patel,
and
H.M.Berman
(1998).
Hydration of the phosphate group in double-helical DNA.
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Biophys J,
75,
2422-2434.
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C.Mayer-Jung,
D.Moras,
and
Y.Timsit
(1998).
Hydration and recognition of methylated CpG steps in DNA.
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EMBO J,
17,
2709-2718.
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PDB codes:
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B.Pan,
C.Ban,
M.C.Wahl,
and
M.Sundaralingam
(1997).
Crystal structure of d(GCGCGCG) with 5'-overhang G residues.
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Biophys J,
73,
1553-1561.
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PDB code:
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M.C.Wahl,
and
M.Sundaralingam
(1997).
Crystal structures of A-DNA duplexes.
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Biopolymers,
44,
45-63.
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B.Hartmann,
and
R.Lavery
(1996).
DNA structural forms.
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Q Rev Biophys,
29,
309-368.
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C.Ban,
and
M.Sundaralingam
(1996).
Crystal structure of the self-complementary 5'-purine start decamer d(GCACGCGTGC) in the A-DNA conformation. II.
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Biophys J,
71,
1222-1227.
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PDB code:
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B.Ramakrishnan,
and
M.Sundaralingam
(1995).
Crystal structure of the A-DNA decamer d(CCIGGCCm5CGG) at 1.6 A showing the unexpected wobble I.m5C base pair.
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Biophys J,
69,
553-558.
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PDB code:
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M.A.Young,
G.Ravishanker,
D.L.Beveridge,
and
H.M.Berman
(1995).
Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes.
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Biophys J,
68,
2454-2468.
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M.Suzuki,
and
N.Yagi
(1995).
Stereochemical basis of DNA bending by transcription factors.
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Nucleic Acids Res,
23,
2083-2091.
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N.Spink,
C.M.Nunn,
J.Vojtechovsky,
H.M.Berman,
and
S.Neidle
(1995).
Crystal structure of a DNA decamer showing a novel pseudo four-way helix-helix junction.
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Proc Natl Acad Sci U S A,
92,
10767-10771.
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PDB code:
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V.Fritsch,
A.De Mesmaeker,
A.Waldner,
J.Lebreton,
M.J.Blommers,
and
R.M.Wolf
(1995).
Molecular mechanics and dynamics studies on two structurally related amide-modified DNA backbones for antisense technology.
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Bioorg Med Chem,
3,
321-335.
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Y.G.Gao,
H.Robinson,
J.H.van Boom,
and
A.H.Wang
(1995).
Influence of counter-ions on the crystal structures of DNA decamers: binding of [Co(NH3)6]3+ and Ba2+ to A-DNA.
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Biophys J,
69,
559-568.
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PDB codes:
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C.Ban,
B.Ramakrishnan,
and
M.Sundaralingam
(1994).
Crystal structure of the highly distorted chimeric decamer r(C)d(CGGCGCCG)r(G).spermine complex--spermine binding to phosphate only and minor groove tertiary base-pairing.
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Nucleic Acids Res,
22,
5466-5476.
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PDB code:
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X.Chen,
B.Ramakrishnan,
S.T.Rao,
and
M.Sundaralingam
(1994).
Binding of two distamycin A molecules in the minor groove of an alternating B-DNA duplex.
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Nat Struct Biol,
1,
169-175.
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PDB code:
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
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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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