Structural variability and new intermolecular interactions of Z-DNA in crystals of d(pCpGpCpGpCpG)

Lucy Malinina, Valya Tereshko, Eugeniya Ivanova, Juan A. Subirana, Valya Zarytova, Yurii Nekrasov

Research output: Contribution to journalArticlepeer-review

13 Scopus citations

Abstract

We have determined the single crystal x-ray structure of the synthetic DNA hexamer d(pCpGpCpGpCpG) in two different crystal forms. The hexamer pCGCGCG has the Z-DNA conformation and in both cases the asymmetric unit contains more than one Z-DNA duplex. Crystals belong to the space group C2221 with a = 69.73, b = 52.63, and c = 26.21 Å, and to the space group P21 with a = 49.87, b = 41.26, c = 21.91 Å, and γ = 97.12°. Both crystals show new crystal packing modes. The molecules also show striking new features when compared with previously determined Z-DNA structures: 1) the bases in one duplex have a large inclination with respect to the helical axis, which alters the overall shape of the molecule. 2) Some cytosine nitrogens interact by hydrogen bonding with phosphates in neighbor molecules. Similar base- phosphate interactions had been previously detected in some B-DNA crystals. 3) Basepair stacking between the ends of neighbor molecules is variable and no helical continuity is maintained between contiguous hexamer duplexes.

Original languageEnglish (US)
Pages (from-to)2482-2490
Number of pages9
JournalBiophysical journal
Volume74
Issue number5
DOIs
StatePublished - May 1998

Bibliographical note

Funding Information:
This work was supported by Grants INTAS-93-2755, RFBR-96-04-49383, and DGICYT-PB93-1067, and grants from Comissariat per Universitats i Recerca de la Generalitat de Catalunya and CESCA for free computer time.

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