Structural variability of a-dna in crystals of the octamer d(pcpcpcpgpcpgpgpg)

Luzimar G. Fernandez, Juan A. Subirana, Nuria Verdaguer, Dmitrii Pyshnyi, Lourdes Campos, Lucy Malinina

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17 Scopus citations


We have determined the structure of the synthetic DNA octamer d(pCpCpCpGpCpGpGpG) in five different crystal forms by single crystal X-ray diffraction. One crystal belongs to the space group P43212 with a=b=41.77, c=25.15 Å, whereas all others have the space group P212121 with progressively decreasing unit cell volumes. In all crystals the octamer forms duplexes of A-DNA and all crystals display a similar packing mode, typical for A-DNA. The structure of the duplex varies from loose to very compact when going from one crystal form to another. The most compact form exhibits a volume of 995 Å3 per base pair. Such a high density has never been found in A-DNA, being more characteristic of Z-DNA crystals. A comparison of the most with the least compact forms gives a RMS value of 1.7 Å, with the distance between the phosphate centers through the major groove being almost twice shorter in the compact form. The phosphate-phosphate separation across the major groove in the compact form is extremely small, 0.7Å. The helical parameters also vary significantly in the various crystal forms. Differences in the helical twist can reach 13° in the same step of the octamer in different crystal forms. The results prove that A-DNA is structurally very variable and demonstrate that the local structure of the same DNA fragment can strongly depend on the crystal environment.

Original languageEnglish (US)
Pages (from-to)151-163
Number of pages13
JournalJournal of Biomolecular Structure and Dynamics
Issue number1
StatePublished - Aug 1997
Externally publishedYes

Bibliographical note

Funding Information:
This work has been supported by grants INTAS-93-2755, RFFI-96-04-49383 and DGICYT PB93-1067. Support from the Comissionat de Recerca de Ia Generalitat de Catalunya is also acknowledged. Part of this work was carried out while LM was a visiting professor at the UPC. LGF was a recipient of a fellowship from the Institute de Cooperaci6n Iberoamericano.


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