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PDBsum entry 1aff
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PDB id:
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DNA
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Title:
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DNA quadruplex containing gggg tetrads and (t.A).A triads, nmr, 8 structures
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Structure:
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Quadruplex DNA (5'-d(tp Ap Gp G)-3'). Chain: a, b, c, d. Engineered: yes
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Source:
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Synthetic: yes. Other_details: truncated biological sequence
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NMR struc:
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8 models
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Authors:
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A.Kettani,S.Bouaziz,W.Wang,R.A.Jones,D.J.Patel
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Key ref:
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A.Kettani
et al.
(1997).
Bombyx mori single repeat telomeric DNA sequence forms a G-quadruplex capped by base triads.
Nat Struct Biol,
4,
382-389.
PubMed id:
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Date:
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06-Mar-97
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Release date:
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20-Aug-97
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Headers
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References
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T-A-G-G
4 bases
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T-A-G-G
4 bases
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T-A-G-G
4 bases
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T-A-G-G
4 bases
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Nat Struct Biol
4:382-389
(1997)
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PubMed id:
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Bombyx mori single repeat telomeric DNA sequence forms a G-quadruplex capped by base triads.
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A.Kettani,
S.Bouaziz,
W.Wang,
R.A.Jones,
D.J.Patel.
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ABSTRACT
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A combined NMR-molecular dynamics approach has been applied to determine the
solution structure of a truncated analogue of the Bombyx mori telomeric d(TTAGG)
single repeat sequence in Na+ cation-containing aqueous solution. The two-fold
symmetric four-stranded d(TAGG) quadruplex contains two adjacent
G(syn).G(syn).G(anti).G(anti) G-tetrads sandwiched between novel (T.A).A triads
with individual strands having both a parallel and antiparallel neighbour around
the quadruplex. The (T.A).A triad represents the first experimental verification
of a base triad alignment which constitutes a key postulate in the recently
proposed model of triad-DNA. Further, the (T.A).A triad is generated by
positioning an A residue through hydrogen bonding in the minor groove of a
Watson-Crick T.A base pair and includes a T-A platform related to an A-A
platform recently observed in the structure of the P4-P6 domain of the
Tetrahymena self splicing group I ribozyme. The novel architecture of the
truncated Bombyx mori quadruplex structure sets the stage for the design and
potential identification of additional base tetrads and triads that could
participate in pairing alignments of multi-stranded DNA structures during
chromosome association and genetic recombination.
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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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R.Basundra,
A.Kumar,
S.Amrane,
A.Verma,
A.T.Phan,
and
S.Chowdhury
(2010).
A novel G-quadruplex motif modulates promoter activity of human thymidine kinase 1.
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FEBS J,
277,
4254-4264.
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S.Amrane,
R.W.Ang,
Z.M.Tan,
C.Li,
J.K.Lim,
J.M.Lim,
K.W.Lim,
and
A.T.Phan
(2009).
A novel chair-type G-quadruplex formed by a Bombyx mori telomeric sequence.
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Nucleic Acids Res,
37,
931-938.
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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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J.T.Nielsen,
K.Arar,
and
M.Petersen
(2006).
NMR solution structures of LNA (locked nucleic acid) modified quadruplexes.
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Nucleic Acids Res,
34,
2006-2014.
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PDB codes:
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A.T.Phan,
V.Kuryavyi,
H.Y.Gaw,
and
D.J.Patel
(2005).
Small-molecule interaction with a five-guanine-tract G-quadruplex structure from the human MYC promoter.
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Nat Chem Biol,
1,
167-173.
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PDB codes:
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V.Dapić,
V.Abdomerović,
R.Marrington,
J.Peberdy,
A.Rodger,
J.O.Trent,
and
P.J.Bates
(2003).
Biophysical and biological properties of quadruplex oligodeoxyribonucleotides.
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Nucleic Acids Res,
31,
2097-2107.
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J.Sühnel
(2001).
Beyond nucleic acid base pairs: from triads to heptads.
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Biopolymers,
61,
32-51.
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T.Simonsson
(2001).
G-quadruplex DNA structures--variations on a theme.
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Biol Chem,
382,
621-628.
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M.A.Keniry
(2000).
Quadruplex structures in nucleic acids.
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Biopolymers,
56,
123-146.
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T.Simonsson,
and
R.Sjöback
(1999).
DNA tetraplex formation studied with fluorescence resonance energy transfer.
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J Biol Chem,
274,
17379-17383.
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T.Simonsson,
P.Pecinka,
and
M.Kubista
(1998).
DNA tetraplex formation in the control region of c-myc.
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Nucleic Acids Res,
26,
1167-1172.
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A.Lebrun,
and
R.Lavery
(1997).
Unusual DNA conformations.
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Curr Opin Struct Biol,
7,
348-354.
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C.H.Lin,
and
D.J.Patel
(1997).
Structural basis of DNA folding and recognition in an AMP-DNA aptamer complex: distinct architectures but common recognition motifs for DNA and RNA aptamers complexed to AMP.
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Chem Biol,
4,
817-832.
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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
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
