Structure of the oligonucleotide d(CGTATATACG) as a site-specific complex with nickel ions

Nicola G.A. Abrescia, Lucy Malinina, Luzimar G. Fernandez, Tam Huynh-Dinh, Stephen Neidle, Juan A. Subirana

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66 Scopus citations

Abstract

In this paper we explore the application of Ni2+ to the crystallization of oligonucleotides. We have determined in this way the structure of a fully alternating (Y-R) decanucleotide d(CGTATATACG) by single crystal X-ray diffraction. This is the first oligonucleotide crystal structure with an alternating 5'-(TA)3-3' central part. Alternating oligonucleotides have a particular interest since they often have a unique structure. In this case the general conformation is B-like with an alternating twist and an end-to-end interaction which involves terminal guanines. The crystal belongs to space group P41212 with a = b = 52.46, c= 101.49 Å. This packing imposes a 90°crossing of the symmetry related helices. This is a new way of packing for decamers. The oligonucleotide structure is characterized by the specific association with seven nickel ions, involving the N7 atom of every guanine. One of the Ni2+ ions is shared between two guanines of symmetry related molecules. Until now no oligonucleotide has been crystallized in the presence of this metal ion. A novel C·A·T triplet structure has also been tentatively identified.

Original languageEnglish (US)
Pages (from-to)1593-1599
Number of pages7
JournalNucleic acids research
Volume27
Issue number7
DOIs
StatePublished - Apr 1 1999

Bibliographical note

Funding Information:
We are very grateful to Drs Valya Tereshko and Lourdes Campos for constant interest and help at various stages of this work. Dr Christine Nunn is also thanked for useful and interesting discussions. This work was supported by grant DGICYT-PB93-1067 and support from the Commissionat per Universitat i Recerca de la Generalitat de Catalunya. N.G.A.A. is a recipient of a Marie Curie predoctoral fellowship. N.G.A.A. thanks the British Council for partial support of his travel expenses at The Institute of Cancer Research.

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