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Crystal and molecular structure of the ammonium salt of the dinucleoside monophosphate d(CpG)

Ramakrishnan, B and Viswamitra, MA (1988) Crystal and molecular structure of the ammonium salt of the dinucleoside monophosphate d(CpG). In: Journal of Biomolecular Structure & Dynamics, 6 (3). pp. 511-523.

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Official URL: http://www.ncbi.nlm.nih.gov/pubmed/3271536


The crystal and molecular structure of the ammonium salt of deoxycytidylyl-(3'-5')-deoxyguanosine has been determined from 0.85 A resolution single crystal X-ray diffraction data. The crystals obtained by acetone diffusion technique at -20 degrees C, are orthorhombic, P212121, a = 12.880(2), b = 17444(2) and c = 27.642(2) A. The structure was solved by high resolution Patterson and Fourier methods and refined to R = 0.136. There are two d(CpG) molecules in the asymmetric unit forming a mini left handed Z-DNA helix. This is in contrast to the earlier reported forms of d(CpG) where the molecules form self base paired duplexes. There are two ammonium ions in the asymmetric unit. The major groove NH+4 ion interacts with N7 of guanines through water bridges besides making H-bonded interactions directly with the phosphate oxygen atoms. A second NH+4 ion is found in the minor groove interacting directly with the phosphate oxygen atoms. Symmetry related molecules pack in such a way that the cytosine base stacks on cytosine and guanine base on guanine. Our structure demonstrates that alternating d(CpG) sequences have the ability to adopt the left handed Z-DNA structure even at the dimer level i.e., in a sequence which is only two base pairs long.

Item Type: Journal Article
Publication: Journal of Biomolecular Structure & Dynamics
Publisher: Adenine Press
Additional Information: Copyright of this article belongs to Adenine Press.
Department/Centre: Division of Biological Sciences > Molecular Reproduction, Development & Genetics
Division of Physical & Mathematical Sciences > Physics
Date Deposited: 07 Sep 2010 06:54
Last Modified: 07 Sep 2010 06:54
URI: http://eprints.iisc.ac.in/id/eprint/32077

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