Crystal Structure of Guanylyl-$2^\prime,5^\prime$-Cytidine Dihydrate: An Analogue of msDNA-RNA Junction in Stigmatella aurantiaca

Krishnan, R and Seshadri, TP (1994) Crystal Structure of Guanylyl-$2^\prime,5^\prime$-Cytidine Dihydrate: An Analogue of msDNA-RNA Junction in Stigmatella aurantiaca. In: Biopolymers, 34 (12). pp. 1637-1646.

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Abstract

Sequence analysis of msDNA from bacterium such as Stigmatella aurantiaca, Myxococcus xanthus and Escherichia coli B revealed that the guanine residue of the single-stranded RNA is linked to the cytosine residue of the msDNA through a $2^\prime,5^\prime$ instead of a conventional $3^\prime,5^\prime$ phosphodiester bond. We have now obtained the crystal structure of the self-complementary dimer guanylyl-$2^\prime,5^\prime$-cytidine $(G2^\prime p 5^\prime C)$ that occurs at the msDNA-RNA junction. $(G2^\prime p 5^\prime C)$ crystallizes in the orthorhombic space group $P2_12_12_1$ with a = 8.376(2), b = 16.231(5), c = 18.671(4). CuK \alpha intensity data were collected on a diffractometer in the $\omega -2\theta$; scan mode. The amount of 1699 out of 2354 reflections having $I \geq 3\sigma (F)$ were considered observed. The structure was solved by direct methods and refined by full-matrix least squares to a R factor of 0.054. The conformation of the guanine base about the glycosyl bond is syn $(X_1 = -54)$ and that of cytosine is anti $(X_2 = 156)$. The $2^\prime and 5^\prime$ and ribose moieties show $C2^\prime $-endo and C3-endo mixed puckering just like in $A2^\prime p 5^\prime A$, $A2^\prime p 5^\prime C$, $A2^\prime p 5^\prime U$, and $d3^\prime p 5^\prime G$. Charge neutralization in $(G2^\prime p 5^\prime C)$ is accomplished through protonation of the cytosine base. An important feature of $G2^\prime p 5^\prime C$ is the stacking of guanine on ribose $ 04^\prime $ of cytosine similar to that seen in other $2^\prime,5^\prime$ dimers. $(G2^\prime p 5^\prime C)$, unlike its $3^\prime,5^\prime$ isomer, does not form a miniature double helix with the Watson-Crick base-pairing pattern. Comparison of $G2^\prime p 5^\prime C$ with $A2^\prime p 5^\prime C$ reveals that they are isostructural. A branched trinucleotide model for the msDNA-RNA junction has been postulated.

Item Type:	Journal Article
Publication:	Biopolymers
Publisher:	John Wiley & Sons, Inc.
Additional Information:	The copyright belongs to John Wiley & Sons, Inc.
Department/Centre:	Division of Physical & Mathematical Sciences > Physics
Date Deposited:	01 Dec 2005
Last Modified:	19 Sep 2010 04:21
URI:	http://eprints.iisc.ac.in/id/eprint/4074

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