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Overview of the Structure of All-AT Oligonucleotides: Organization in Helices and Packing Interactions

Lourdes Campos ^*, Núria Valls ^*, Lourdes Urpí ^*, Catherine Gouyette , Trinidad Sanmartín ^*, Michael Richter ^*, Elida Alechaga ^*, Alicia Santaolalla ^*, Roberto Baldini ^*, Marc Creixell ^*, Ruth Ciurans ^*, Petr Skokan ^*, Joan Pous  and Juan A. Subirana ^*

^* Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, E-08028 Barcelona, Spain; Plate-forme de synthèse d'oligonucléotides, Institut Pasteur, 75724 Paris, France; and Plataforma Automatitzada de Cristal.lografia, PCB-CSIC, E-08028 Barcelona, Spain

Correspondence: Address reprint requests to J. A. Subirana, Tel:. 34-934-016-688; Fax: 34-934-010-978; E-mail: juan.a.subirana{at}upc.edu.

We present the crystalline organization of 33 all-AT deoxyoligonucleotide duplexes, studied by x-ray diffraction. Most of them have very similar structures, with Watson-Crick basepairs and a standard average twist close to 36°. The molecules are organized as parallel columns of stacked duplexes in a helical arrangement. Such organization of duplexes is very regular and repetitive: all sequences show the same pattern. It is mainly determined by the stacking of the terminal basepairs, so that the twist in the virtual TA base step between neighbor duplexes is always negative, –22°. The distance between the axes of parallel columns is practically identical in all cases, 26 Å. Interestingly, it coincides with that found in DNA viruses and fibers in their hexagonal phase. It appears to be a characteristic distance for ordered parallel DNA molecules. This feature is due to the absence of short range intermolecular forces, which are usually due to the presence of CG basepairs at the end of the oligonucleotide sequence. The duplexes apparently interact only through their diffuse ionic atmospheres. The results obtained can thus be considered as intermediate between liquid crystals, fibers, and standard crystal structures. They provide new information on medium range DNA-DNA interactions.