An A-DNA structure with two independent duplexes in the asymmetric unit

Savitha, G and Viswamitra, MA (1999) An A-DNA structure with two independent duplexes in the asymmetric unit. In: Acta Crystallographica Section D: Biological Crystallography, 55 (6). pp. 1136-1143.

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Abstract

The crystal and molecular structure of the self-complementary A-DNA decamer sequence $d(G_4CGC_4)$ was solved at 1.9 \AA resolution. The decamer crystallizes in space group $P2_1$ with two independent duplexes in the asymmetric unit. Duplex 1 has interactions which are distributed symmetrically about its length compared with duplex 2. The two end base pairs of duplex 1 have a similar NH O hydrogen-bond pattern involving GGC segments of duplex 2 and a symmetry-related neighbour, while the end base pairs of duplex 2 interact with the GCC and GGG segments of its symmetry-related neighbours through NH...O and NH...N hydrogen bonds and a water-mediated hydrogen bond between the carboxyl groups of C40 and C8. In addition to the C4'-C5' torsion angle \gamma assuming the trans conformation in certain steps, this angle also adopts the $gauche^-$ conformation at C37 as opposed to the preferred $gauche^+$ conformation, with a concomitant change in phosphodiester P-O5' $(\alpha)$ in the opposite sense. This facilitates stacking between adjacent bases. The study suggests that the structural alterations in the two molecules in the asymmetric unit originate from an inherent propensity of the $d(G_4CGC_4)$ base sequence for varied intermolecular interactions and malleability.

Item Type:	Journal Article
Publication:	Acta Crystallographica Section D: Biological Crystallography
Publisher:	International Union of Crystallography
Additional Information:	Copyright of this article belongs to International Union of Crystallography.
Department/Centre:	Division of Physical & Mathematical Sciences > Physics
Date Deposited:	16 Oct 2007
Last Modified:	19 Sep 2010 04:40
URI:	http://eprints.iisc.ac.in/id/eprint/12088

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