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PDBsum entry 200d
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DOI no:
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Proc Natl Acad Sci U S A
92:3874-3878
(1995)
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PubMed id:
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Stable loop in the crystal structure of the intercalated four-stranded cytosine-rich metazoan telomere.
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C.Kang,
I.Berger,
C.Lockshin,
R.Ratliff,
R.Moyzis,
A.Rich,
A.Rich.
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ABSTRACT
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In most metazoans, the telomeric cytosine-rich strand repeating sequence is
d(TAACCC). The crystal structure of this sequence was solved to 1.9-A
resolution. Four strands associate via the cytosine-containing parts to form a
four-stranded intercalated structure held together by C.C+ hydrogen bonds. The
base-paired strands are parallel to each other, and the two duplexes are
intercalated into each other in opposite orientations. One TAA end forms a
highly stabilized loop with the 5' thymine Hoogsteen-base-paired to the third
adenine. The 5' end of this loop is in close proximity to the 3' end of one of
the other intercalated cytosine strands. Instead of being entirely in a DNA
duplex, this structure suggests the possibility of an alternative conformation
for the cytosine-rich telomere strands.
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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.Zhou,
C.Wei,
G.Jia,
X.Wang,
Z.Feng,
and
C.Li
(2010).
Formation of i-motif structure at neutral and slightly alkaline pH.
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Mol Biosyst,
6,
580-586.
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M.Kaushik,
M.Prasad,
S.Kaushik,
A.Singh,
and
S.Kukreti
(2010).
Structural transition from dimeric to tetrameric i-motif, caused by the presence of TAA at the 3'-end of human telomeric C-rich sequence.
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Biopolymers,
93,
150-160.
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B.Sridhar,
and
K.Ravikumar
(2008).
Supramolecular hydrogen-bonded networks in cytosinium succinate and cytosinium 4-nitrobenzoate cytosine monohydrate.
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Acta Crystallogr C,
64,
o566-o569.
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F.Seela,
and
S.Budow
(2008).
Mismatch formation in solution and on DNA microarrays: how modified nucleosides can overcome shortcomings of imperfect hybridization caused by oligonucleotide composition and base pairing.
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Mol Biosyst,
4,
232-245.
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F.Seela,
S.Budow,
and
P.Leonard
(2007).
Oligonucleotides forming an i-motif: the pH-dependent assembly of individual strands and branched structures containing 2'-deoxy-5-propynylcytidine.
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Org Biomol Chem,
5,
1858-1872.
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J.Völker,
H.H.Klump,
and
K.J.Breslauer
(2007).
The energetics of i-DNA tetraplex structures formed intermolecularly by d(TC5) and intramolecularly by d[(C5T3)3C5].
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Biopolymers,
86,
136-147.
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P.S.Pallan,
P.Lubini,
M.Bolli,
and
M.Egli
(2007).
Backbone-base inclination as a fundamental determinant of nucleic acid self- and cross-pairing.
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Nucleic Acids Res,
35,
6611-6624.
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S.Y.Han,
S.H.Lee,
J.Chung,
and
H.B.Oh
(2007).
Base-pair interactions in the gas-phase proton-bonded complexes of C(+)G and C(+)GC.
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J Chem Phys,
127,
245102.
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S.Modi,
A.H.Wani,
and
Y.Krishnan
(2006).
The PNA-DNA hybrid I-motif: implications for sugar-sugar contacts in i-motif tetramerization.
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Nucleic Acids Res,
34,
4354-4363.
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G.V.Tolstonog,
G.Li,
R.L.Shoeman,
and
P.Traub
(2005).
Interaction in vitro of type III intermediate filament proteins with higher order structures of single-stranded DNA, particularly with G-quadruplex DNA.
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DNA Cell Biol,
24,
85.
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J.A.Brazier,
J.Fisher,
and
R.Cosstick
(2005).
Stabilization of the DNA I-motif structure by incorporation of 3'-S-phosphorothiolate linkages.
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Angew Chem Int Ed Engl,
45,
114-117.
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N.K.Sharma,
and
K.N.Ganesh
(2005).
PNA C-C+ i-motif: superior stability of PNA TC8 tetraplexes compared to DNA TC8 tetraplexes at low pH.
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Chem Commun (Camb),
(),
4330-4332.
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Y.Zhao,
Z.X.Zeng,
Z.Y.Kan,
Y.H.Hao,
and
Z.Tan
(2005).
The folding and unfolding kinetics of the i-motif structure formed by the C-rich strand of human telomere DNA.
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Chembiochem,
6,
1957-1960.
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B.Pan,
Y.Xiong,
K.Shi,
and
M.Sundaralingam
(2003).
An eight-stranded helical fragment in RNA crystal structure: implications for tetraplex interaction.
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Structure,
11,
825-831.
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PDB code:
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G.W.Han,
M.L.Kopka,
D.Langs,
M.R.Sawaya,
and
R.E.Dickerson
(2003).
Crystal structure of an RNA.DNA hybrid reveals intermolecular intercalation: dimer formation by base-pair swapping.
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Proc Natl Acad Sci U S A,
100,
9214-9219.
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PDB code:
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G.Savitha,
D.Leonidas,
K.R.Acharya,
and
M.A.Viswamitra
(2001).
Crystallization and preliminary investigations on a telomeric repeat sequence C4A2C4A2.
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Acta Crystallogr D Biol Crystallogr,
57,
873-875.
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K.Kanaori,
N.Shibayama,
K.Gohda,
K.Tajima,
and
K.Makino
(2001).
Multiple four-stranded conformations of human telomere sequence d(CCCTAA) in solution.
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Nucleic Acids Res,
29,
831-840.
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M.Perbandt,
M.Vallazza,
C.Lippmann,
C.Betzel,
and
V.A.Erdmann
(2001).
Structure of an RNA duplex with an unusual G.C pair in wobble-like conformation at 1.6 A resolution.
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Acta Crystallogr D Biol Crystallogr,
57,
219-224.
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PDB code:
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F.Geinguenaud,
J.Liquier,
M.G.Brevnov,
O.V.Petrauskene,
Y.I.Alexeev,
E.S.Gromova,
and
E.Taillandier
(2000).
Parallel self-associated structures formed by T,C-rich sequences at acidic pH.
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Biochemistry,
39,
12650-12658.
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M.Guéron,
and
J.L.Leroy
(2000).
The i-motif in nucleic acids.
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Curr Opin Struct Biol,
10,
326-331.
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J.Weil,
T.Min,
C.Yang,
S.Wang,
C.Sutherland,
N.Sinha,
and
C.Kang
(1999).
Stabilization of the i-motif by intramolecular adenine-adenine-thymine base triple in the structure of d(ACCCT).
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Acta Crystallogr D Biol Crystallogr,
55,
422-429.
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PDB codes:
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D.Schlessinger,
and
R.Nagaraja
(1998).
Impact and implications of yeast and human artificial chromosomes.
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Ann Med,
30,
186-191.
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K.Kanaori,
A.Maeda,
H.Kanehara,
K.Tajima,
and
K.Makino
(1998).
1H nuclear magnetic resonance study on equilibrium between two four-stranded solution conformations of short d(CnT).
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Biochemistry,
37,
12979-12986.
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S.Neidle,
and
C.M.Nunn
(1998).
Crystal structures of nucleic acids and their drug complexes.
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Nat Prod Rep,
15,
1.
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W.Shepard,
W.B.Cruse,
R.Fourme,
E.de la Fortelle,
and
T.Prangé
(1998).
A zipper-like duplex in DNA: the crystal structure of d(GCGAAAGCT) at 2.1 A resolution.
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Structure,
6,
849-861.
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PDB code:
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I.Berger,
L.Cai,
L.Chen,
A.Rich,
and
A.Rich
(1997).
Energetics of the lattice: packing elements in crystals of four-stranded intercalated cytosine-rich DNA molecules.
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Biopolymers,
44,
257-267.
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S.Nonin,
A.T.Phan,
and
J.L.Leroy
(1997).
Solution structure and base pair opening kinetics of the i-motif dimer of d(5mCCTTTACC): a noncanonical structure with possible roles in chromosome stability.
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Structure,
5,
1231-1246.
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PDB code:
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I.Berger,
M.Egli,
and
A.Rich
(1996).
Inter-strand C-H...O hydrogen bonds stabilizing four-stranded intercalated molecules: stereoelectronic effects of O4' in cytosine-rich DNA.
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Proc Natl Acad Sci U S A,
93,
12116-12121.
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J.M.Benevides,
C.Kang,
and
G.J.Thomas
(1996).
Raman signature of the four-stranded intercalated cytosine motif in crystal and solution structures of DNA deoxycytidylates d(CCCT) and d(C8).
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Biochemistry,
35,
5747-5755.
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L.Lacroix,
J.L.Mergny,
J.L.Leroy,
and
C.Hélène
(1996).
Inability of RNA to form the i-motif: implications for triplex formation.
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Biochemistry,
35,
8715-8722.
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D.Rhodes,
and
R.Giraldo
(1995).
Telomere structure and function.
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Curr Opin Struct Biol,
5,
311-322.
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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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Links
