1k4x
From Proteopedia
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POTASSIUM FORM OF OXY-1.5 QUADRUPLEX DNA
Overview
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.
About this Structure
1K4X is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
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))., Schultze P, Hud NV, Smith FW, Feigon J, Nucleic Acids Res. 1999 Aug 1;27(15):3018-28. PMID:10454595
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