1S47

Crystal structure analysis of the DNA quadruplex d(TGGGGT)S2

1S47 の概要

• エントリーDOI: 10.2210/pdb1s47/pdb
• 分子名称: 5'-D(*TP*GP*GP*GP*GP*T)-3', SODIUM ION, THALLIUM (I) ION, ... (4 entities in total)
• 機能のキーワード: quadruplex dna, thymine triads and tetrads, thallium, dna
• タンパク質・核酸の鎖数: 12
• 化学式量合計: 23950.24

構造登録者

Caceres, C.,Wright, G.,Gouyette, C.,Parkinson, G.,Subirana, J.A. (登録日: 2004-01-15, 公開日: 2004-02-24, 最終更新日: 2023-08-23)

主引用文献

Caceres, C.,Wright, G.,Gouyette, C.,Parkinson, G.,Subirana, J.A.
A Thymine tetrad in d(TGGGGT) quadruplexes stabilized with Tl+1/Na+1 ions
Nucleic Acids Res., 32:1097-1102, 2004

PubMed Abstract: 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.

PubMed: 14960719
DOI: 10.1093/nar/gkh269

実験手法

X-RAY DIFFRACTION (2.5 Å)