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PDBsum entry 2avh
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J Am Chem Soc
128:5480-5487
(2006)
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PubMed id:
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Topology variation and loop structural homology in crystal and simulated structures of a bimolecular DNA quadruplex.
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P.Hazel,
G.N.Parkinson,
S.Neidle.
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ABSTRACT
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The topology of DNA quadruplexes depends on the nature and number of the
nucleotides linking G-quartet motifs. To assess the effects of a
three-nucleotide TTT linker, the crystal structure of the DNA sequence
d(G(4)T(3)G(4)) has been determined at 1.5 A resolution, together with that of
the brominated analogue d(G(4)(Br)UTTG(4)) at 2.4 A resolution. Both sequences
form bimolecular intermolecular G-quadruplexes with lateral loops.
d(G(4)(Br)UTTG(4)) crystallized in the monoclinic space group P2(1) with three
quadruplex molecules in the asymmetric unit, two associating together as a
head-to-head stacked dimer, and the third as a single head-to-tail dimer. The
head-to-head dimers have two lateral loops on the same G-quadruplex face and
form an eight-G-quartet stack, with a linear array of seven K(+) ions between
the quartets. d(G(4)T(3)G(4)) crystallized in the orthorhombic space group C222
and has a structure very similar to the head-to-tail dimer in the P2(1) unit
cell. The sequence studied here is able to form several different folds;
however, all four quadruplexes in the two structures have lateral loops, in
contrast to the diagonal loops reported for the analogous quadruplex with T(4)
loops. A total of seven independent T(3) loops were observed in the two
structures. These can be classified into two discrete conformational classes,
suggesting that these represent preferred loop conformations that are
independent of crystal-packing forces.
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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.Amato,
G.Oliviero,
E.De Pauw,
and
V.Gabelica
(2009).
Hybridization of short complementary PNAs to G-quadruplex forming oligonucleotides: An electrospray mass spectrometry study.
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Biopolymers,
91,
244-255.
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S.T.Hsu,
P.Varnai,
A.Bugaut,
A.P.Reszka,
S.Neidle,
and
S.Balasubramanian
(2009).
A G-rich sequence within the c-kit oncogene promoter forms a parallel G-quadruplex having asymmetric G-tetrad dynamics.
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J Am Chem Soc,
131,
13399-13409.
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PDB codes:
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D.J.Patel,
A.T.Phan,
and
V.Kuryavyi
(2007).
Human telomere, oncogenic promoter and 5'-UTR G-quadruplexes: diverse higher order DNA and RNA targets for cancer therapeutics.
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Nucleic Acids Res,
35,
7429-7455.
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P.A.Rachwal,
I.S.Findlow,
J.M.Werner,
T.Brown,
and
K.R.Fox
(2007).
Intramolecular DNA quadruplexes with different arrangements of short and long loops.
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Nucleic Acids Res,
35,
4214-4222.
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P.Auffinger,
and
Y.Hashem
(2007).
Nucleic acid solvation: from outside to insight.
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Curr Opin Struct Biol,
17,
325-333.
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R.Ida,
I.C.Kwan,
and
G.Wu
(2007).
Direct 23Na NMR observation of mixed cations residing inside a G-quadruplex channel.
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Chem Commun (Camb),
(),
795-797.
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S.Burge,
G.N.Parkinson,
P.Hazel,
A.K.Todd,
and
S.Neidle
(2006).
Quadruplex DNA: sequence, topology and structure.
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Nucleic Acids Res,
34,
5402-5415.
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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
codes are
shown on the right.
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Links
