1s47
From Proteopedia
(New page: 200px<br /><applet load="1s47" size="450" color="white" frame="true" align="right" spinBox="true" caption="1s47, resolution 2.50Å" /> '''Crystal structure an...) |
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| - | [[Image:1s47.gif|left|200px]]<br /><applet load="1s47" size=" | + | [[Image:1s47.gif|left|200px]]<br /><applet load="1s47" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1s47, resolution 2.50Å" /> | caption="1s47, resolution 2.50Å" /> | ||
'''Crystal structure analysis of the DNA quadruplex d(TGGGGT)S2'''<br /> | '''Crystal structure analysis of the DNA quadruplex d(TGGGGT)S2'''<br /> | ||
==Overview== | ==Overview== | ||
| - | We report two new structures of the quadruplex d(TGGGGT)4 obtained by | + | We report two new structures of the quadruplex d(TGGGGT)4 obtained by single crystal X-ray diffraction. In one of them a thymine tetrad is found. Thus the yeast telomere sequences d(TG1-3) might be able to form continuous quadruplex structures, involving both guanine and thymine tetrads. Our study also shows substantial differences in the arrangement of thymines when compared with previous studies. We find five different types of organization: (i) groove binding with hydrogen bonds to guanines from a neighbour quadruplex; (ii) partially ordered groove binding, without any hydrogen bond; (iii) stacked thymine triads, formed at the 3'ends of the quadruplexes; (iv) a thymine tetrad between two guanine tetrads. Thymines are stabilized in pairs by single hydrogen bonds. A central sodium ion interacts with two thymines and contributes to the tetrad structure. (v) Completely disordered thymines which do not show any clear location in the crystal. The tetrads are stabilized by either Na+ or Tl+ ions. We show that by using MAD methods, Tl+ can be unambiguously located and distinguished from Na+. We can thus determine the preference for either ion in each ionic site of the structure under the conditions used by us. |
==About this Structure== | ==About this Structure== | ||
| - | 1S47 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with NA and TL as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http:// | + | 1S47 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=NA:'>NA</scene> and <scene name='pdbligand=TL:'>TL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S47 OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Gouyette, C.]] | [[Category: Gouyette, C.]] | ||
[[Category: Parkinson, G.]] | [[Category: Parkinson, G.]] | ||
| - | [[Category: Subirana, J | + | [[Category: Subirana, J A.]] |
[[Category: Wright, G.]] | [[Category: Wright, G.]] | ||
[[Category: NA]] | [[Category: NA]] | ||
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[[Category: thymine triads and tetrads]] | [[Category: thymine triads and tetrads]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:57:43 2008'' |
Revision as of 12:57, 21 February 2008
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Crystal structure analysis of the DNA quadruplex d(TGGGGT)S2
Overview
We report two new structures of the quadruplex d(TGGGGT)4 obtained by single crystal X-ray diffraction. In one of them a thymine tetrad is found. Thus the yeast telomere sequences d(TG1-3) might be able to form continuous quadruplex structures, involving both guanine and thymine tetrads. Our study also shows substantial differences in the arrangement of thymines when compared with previous studies. We find five different types of organization: (i) groove binding with hydrogen bonds to guanines from a neighbour quadruplex; (ii) partially ordered groove binding, without any hydrogen bond; (iii) stacked thymine triads, formed at the 3'ends of the quadruplexes; (iv) a thymine tetrad between two guanine tetrads. Thymines are stabilized in pairs by single hydrogen bonds. A central sodium ion interacts with two thymines and contributes to the tetrad structure. (v) Completely disordered thymines which do not show any clear location in the crystal. The tetrads are stabilized by either Na+ or Tl+ ions. We show that by using MAD methods, Tl+ can be unambiguously located and distinguished from Na+. We can thus determine the preference for either ion in each ionic site of the structure under the conditions used by us.
About this Structure
1S47 is a Protein complex structure of sequences from [1] with and as ligands. Full crystallographic information is available from OCA.
Reference
A thymine tetrad in d(TGGGGT) quadruplexes stabilized with Tl+/Na+ ions., Caceres C, Wright G, Gouyette C, Parkinson G, Subirana JA, Nucleic Acids Res. 2004 Feb 11;32(3):1097-102. Print 2004. PMID:14960719
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