Overview of the structure of all-AT oligonucleotides:
organization in helices and packing interactions
Lourdes Campos 1, Nuria Valls 1, Lourdes Urpi 1, Catherine Gouyette 2, Trinidad Sanmartin 1, Michael Richter 1, Elida Alechaga 1, Alicia Santaolalla 1, Roberto Baldini 1, Marc Creixell 1, Ruth Ciurans 1, Petr Skokan 1, Joan Pous 3 and Juan A Subirana 1*
1 UPC
2 Pasteur Institute
3 PCB-CSIC
* To whom correspondence should be addressed. E-mail: juan.a.subirana{at}upc.edu.
Submitted on February 28, 2006
Revised on March 21, 2006
Accepted on 24 April 2006
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Abstract |
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We present the crystalline organization of thirty three all-AT deoxyoligonucleotide duplexes, studied by X-ray diffraction. Most of them have very similar structures, with Watson-Crick base pairs 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 base pairs, so that the twist in the virtual TA base step between neighbor duplexes is always negative, about -22°. The distance between the axes of parallel columns is practically identical in all cases, about 26Å. 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 base pairs 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.
Key Words:
DNA, DNA viruses, X-ray crystallography, ionic interactions
