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A parallel stranded $2^{\prime}-5^{\prime}$ double helical model for poly A: crystal structure of adenylyl-$2^{\prime},5^{\prime}$-adenosine trihydrate and comparison with the tetrahydrate structure

Krishnan, R and Seshadri, TP (2000) A parallel stranded $2^{\prime}-5^{\prime}$ double helical model for poly A: crystal structure of adenylyl-$2^{\prime},5^{\prime}$-adenosine trihydrate and comparison with the tetrahydrate structure. In: Journal of Molecular Structure, 522 (1-3). pp. 135-143.

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Abstract

$2^{\prime}-5^{\prime}$ are second in importance only to $3^{\prime}-5^{\prime}$ nucleic acids. They have attracted special attention in recent years because of their potential use in the design and synthesis of antisense oligomers. We have now obtained the crystal structure of adenylyl $2^{\prime}-5^{\prime}$ adenosine trihydrate $(A2^{\prime}p5^{\prime} A)$ as sequel to our earlier studies on $(A2^{\prime}p5^{\prime} A)$ tetrahydrate and other $2^{\prime}-5^{\prime}$ dinucleotide structures. $(A2^{\prime}p5^{\prime} A)$ trihydrate crystals belong to the orthorhombic space group $P2_12_1 2_1$ with unit cell dimensions a=9.284 \AA (3), b=15.360 \AA (3) and c=21.610 \AA (3), one nucleotide and three water molecules in the asymmetric unit. CuK\alpha diffractometer data were collected upto sin \theta / \lambda =0.59 $\AA^{-1}$. The structure was solved by direct methods and refined by full matrix least squares to an R value of 0.125. The $5^{\prime}$ and the $2^{\prime}$ end adenine bases are in the syn and anti conformations with respect to their ribose moieties as in the tetrahydrate structure. The syn conformation is stabilized by the $N3–O5^\prime$ intramolecular hydrogen bond. The $5^{\prime}$ and $2^{\prime}$ ribose moieties show $C3^{\prime}$ and $C2^{\prime}$ endo puckering, respectively. The conformation about the phosphodiester bonds for the $5^{\prime}$ and $2^{\prime}$ ends are $g^-$,$g^-$ and about the $C4^{\prime}- C3^{\prime}$ bonds is $g^-t$. Presumably, charge neutralization in $A2^{\prime}p5^{\prime}A $ is achieved through the protonation of the base. Differences in the hydrogen bond network between the two hydrated structures are discussed. A parallel stranded $2^{\prime}-5^{\prime}$ double helical model for poly A bearing strong resemblance to the $3^{\prime}-5^{\prime}$ poly $AH^+$ model earlier proposed from fiber diffraction studies has been proposed.

Item Type: Journal Article
Additional Information: Copyright of this article belongs to Elsevier.
Keywords: Parallel stranded;Double helix;Poly AH;Oligo A;Antiparallel.
Department/Centre: Division of Physical & Mathematical Sciences > Physics
Date Deposited: 25 Aug 2008
Last Modified: 19 Sep 2010 04:49
URI: http://eprints.iisc.ernet.in/id/eprint/15613

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