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PDBsum entry 1bae
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References listed in PDB file
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Key reference
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Title
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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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Authors
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S.Nonin,
A.T.Phan,
J.L.Leroy.
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Ref.
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Structure, 1997,
5,
1231-1246.
[DOI no: ]
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PubMed id
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Abstract
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BACKGROUND: Repetitive cytosine-rich DNA sequences have been identified in
telomeres and centromeres of eukaryotic chromosomes. These sequences play a role
in maintaining chromosome stability during replication and may be involved in
chromosome pairing during meiosis. The C-rich repeats can fold into an 'i-motif'
structure, in which two parallel-stranded duplexes with hemiprotonated C.C+
pairs are intercalated. Previous NMR studies of naturally occurring repeats have
produced poor NMR spectra. This led us to investigate oligonucleotides, based on
natural sequences, to produce higher quality spectra and thus provide further
information as to the structure and possible biological function of the i-motif.
RESULTS: NMR spectroscopy has shown that d(5mCCTTTACC) forms an i-motif dimer of
symmetry-related and intercalated folded strands. The high-definition structure
is computed on the basis of the build-up rates of 29 intraresidue and 35
interresidue nuclear Overhauser effect (NOE) connectivities. The i-motif core
includes intercalated interstrand C.C+ pairs stacked in the order
2*.8/1.7*/1*.7/2.8* (where one strand is distinguished by an asterisk and the
numbers relate to the base positions within the repeat). The TTTA sequences form
two loops which span the two wide grooves on opposite sides of the i-motif core;
the i-motif core is extended at both ends by the stacking of A6 onto C2.C8+. The
lifetimes of pairs C2.C8+ and 5mC1.C7+ are 1 ms and 1 s, respectively, at 15
degrees C. Anomalous exchange properties of the T3 imino proton indicate
hydrogen bonding to A6 N7 via a water bridge. The d(5mCCTTTTCC)
deoxyoligonucleotide, in which position 6 is occupied by a thymidine instead of
an adenine, also forms a symmetric i-motif dimer. However, in this structure the
two TTTT loops are located on the same side of the i-motif core and the C.C+
pairs are formed by equivalent cytidines stacked in the order
8*.8/1.1*/7*.7/2.2*. CONCLUSIONS: Oligodeoxynucleotides containing two C-rich
repeats can fold and dimerize into an i-motif. The change of folding topology
resulting from the substitution of a single nucleoside emphasizes the influence
of the loop residues on the i-motif structure formed by two folded strands.
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Figure 9.
Figure 9. Structure of the [d(5mCCTTTACC)][2] i-motif. (a)
Schematic representation of [d(5mCCTTTACC)][2]. The cytidine
color-coding is the same as in the schematic representation in
Figure 5b, A6 is in green, T3 is in purple, and T4 and T5 are in
blue. The C2 symmetry axis passes through the two non-equivalent
narrow grooves. (b) View of the lowest-energy conformer looking
into the wide groove. (c) View of a superposition of the eight
lowest-energy conformers of [d(5mCCTTTACC)][2], looking into the
narrow groove defined by the 5mC1-C2 segments.
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The above figure is
reprinted
by permission from Cell Press:
Structure
(1997,
5,
1231-1246)
copyright 1997.
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Secondary reference #1
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Title
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Structure and conversion kinetics of a bi-Stable DNA i-Motif: broken symmetry in the [d(5mcctcc)]4 tetramer.
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Authors
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S.Nonin,
J.L.Leroy.
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Ref.
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J Mol Biol, 1996,
261,
399-414.
[DOI no: ]
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PubMed id
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Figure 7.
Figure 7. End-on-view of three hypothetical strand
arrangements in an i-motif tetramer containing two kind
of strands (open and closed circle) in identical
proportions. The strand orientation is indicated by the
symbols w and +. Base-pairing between duplexes is
indicated by thin lines.
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Figure 8.
Figure 8. Schematic representation of the inter-residue distance restraints used to compute the [d(5mCCTCC)]4
structure. The distance restraints between strand 4a5 and strand 4b5, and between strand 4a5 and strand 4d5 define
the inter-strand relations across the wide groove and the narrow groove, respectively. The amino-H2'/H2" and the
H1'-H1' inter-strand connectivities indicated by heavy lines are characteristic of the i-motif structure and determine
the intercalation topology.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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Secondary reference #2
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Title
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Solution structures of the i-Motif tetramers of d(tcc), D(5methylcct) and d(t5methylcc): novel noe connections between amino protons and sugar protons.
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Authors
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J.L.Leroy,
M.Guéron.
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Ref.
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Structure, 1995,
3,
101-120.
[DOI no: ]
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PubMed id
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Figure 10.
Figure 10. Stereoview, normal to the wide groove, of the
lowest-energy conformer of [d(TCC)][4] . T1, green; C2, red; C3
yellow. Figure 10. Stereoview, normal to the wide groove, of
the lowest-energy conformer of [d(TCC)][4] . T1, green; C2, red;
C3 yellow.
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Figure 11.
Figure 11. Views of the eight lowest-energy conformers of the
d(TCC) tetramer. (a) View of the wide groove. (b) View of the
narrow groove. Colour coding as in Figure 10. Figure 11.
Views of the eight lowest-energy conformers of the d(TCC)
tetramer. (a) View of the wide groove. (b) View of the narrow
groove. Colour coding as in [3]Figure 10.
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The above figures are
reproduced from the cited reference
with permission from Cell Press
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Headers
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