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PDBsum entry 1k4x
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References listed in PDB file
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Key reference
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Title
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The effect of sodium, Potassium and ammonium ions on the conformation of the dimeric quadruplex formed by the oxytricha nova telomere repeat oligonucleotide d(g(4)t(4)g(4)).
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Authors
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P.Schultze,
N.V.Hud,
F.W.Smith,
J.Feigon.
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Ref.
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Nucleic Acids Res, 1999,
27,
3018-3028.
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PubMed id
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Abstract
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The DNA sequence d(G(4)T(4)G(4)) [Oxy-1.5] consists of 1.5 units of the repeat
in telomeres of Oxytricha nova and has been shown by NMR and X-ray
crystallographic analysis to form a dimeric quadruplex structure with four
guanine-quartets. However, the structure reported in the X-ray study has a
fundamentally different conformation and folding topology compared to the
solution structure. In order to elucidate the possible role of different
counterions in this discrepancy and to investigate the conformational effects
and dynamics of ion binding to G-quadruplex DNA, we compare results from further
experiments using a variety of counterions, namely K(+), Na(+)and NH(4)(+). A
detailed structure determination of Oxy-1.5 in solution in the presence of
K(+)shows the same folding topology as previously reported with the same
molecule in the presence of Na(+). Both conformations are symmetric dimeric
quadruplexes with T(4)loops which span the diagonal of the end quartets. The
stack of quartets shows only small differences in the presence of K(+)versus
Na(+)counterions, but the T(4)loops adopt notably distinguishable conformations.
Dynamic NMR analysis of the spectra of Oxy-1.5 in mixed Na(+)/K(+)solution
reveals that there are at least three K(+)binding sites. Additional experiments
in the presence of NH(4)(+)reveal the same topology and loop conformation as in
the K(+)form and allow the direct localization of three central ions in the
stack of quartets and further show that there are no specific NH(4)(+)binding
sites in the T(4)loop. The location of bound NH(4)(+)with respect to the
expected coordination sites for Na(+)binding provides a rationale for the
difference observed for the structure of the T(4)loop in the Na(+)form, with
respect to that observed for the K(+)and NH(4)(+)forms.
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Secondary reference #1
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Title
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Quadruplex structure of oxytricha telomeric DNA oligonucleotides.
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Authors
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F.W.Smith,
J.Feigon.
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Ref.
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Nature, 1992,
356,
164-168.
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PubMed id
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Headers
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