Nucleic Acids Research, Vol 27, Issue 15 3018-3028, Copyright © 1999 by Oxford University Press
P Schultze, NV Hud, FW Smith and J Feigon
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.
ARTICLES
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))
Department of Chemistry and Biochemistry and Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA.
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