Cáceres Carmen, Wright Glenford, Gouyette Catherine, Parkinson Gary, Subirana Juan A
Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Avinguda Diagonal 647, E-08028 Barcelona, Spain.
Nucleic Acids Res. 2004 Feb 11;32(3):1097-102. doi: 10.1093/nar/gkh269. Print 2004.
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.
我们报道了通过单晶X射线衍射获得的四链体d(TGGGGT)4的两种新结构。其中一种结构中发现了胸腺嘧啶四联体。因此，酵母端粒序列d(TG1-3)可能能够形成连续的四链体结构，涉及鸟嘌呤和胸腺嘧啶四联体。我们的研究还表明，与之前的研究相比，胸腺嘧啶的排列存在显著差异。我们发现了五种不同类型的结构：(i) 通过氢键与相邻四链体中的鸟嘌呤进行沟结合；(ii) 部分有序的沟结合，没有任何氢键；(iii) 在四链体3'端形成的堆积胸腺嘧啶三联体；(iv) 两个鸟嘌呤四联体之间的胸腺嘧啶四联体。胸腺嘧啶通过单氢键成对稳定。一个中心钠离子与两个胸腺嘧啶相互作用并有助于四联体结构的形成。(v) 完全无序的胸腺嘧啶，在晶体中没有任何明确的位置。四联体通过Na+或Tl+离子稳定。我们表明，通过使用MAD方法，可以明确确定Tl+的位置并将其与Na+区分开来。因此，我们可以在所使用的条件下确定结构中每个离子位点对这两种离子的偏好。
