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Published online 11 February 2004

Nucleic Acids Research, 2004, Vol. 32, No. 3 1097-1102
© 2004 Oxford University Press

A thymine tetrad in d(TGGGGT) quadruplexes stabilized with Tl+/Na+ ions

Carmen Cáceres, Glenford Wright, Catherine Gouyette1, Gary Parkinson2 and Juan A. Subirana*

Departament d’Enginyeria Química, Universitat Politècnica de Catalunya, Avinguda Diagonal 647, E-08028 Barcelona, Spain, 1 Unité de Chimie Organique, Institut Pasteur. 28, rue du Docteur Roux, 75724 Paris Cedex 15, France and 2 Cancer Research UK, Biomolecular Structure Group, School of Pharmacy, University of London, 29–39 Brunswick Square, London WC1N 1AX, UK

*To whom correspondence should be addressed. Tel: +34 934 0166 88; Fax: +34 934 010 978; Email: juan.a.subirana{at}upc.es

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.


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