Crystal structure of guanylyl‐2′,5′‐cytidine dihydrate: An analogue of msDNA‐RNA junction in stigmatella aurantiaca

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′–5′ instead of a conventional 3′–5′ phosphodiester bond. We have now obtained the crystal structure of the self‐complementary dimer guanylyl‐2′,5′‐cytidine (G2′p5′C) that occurs at the msDNA‐RNA junction. G2′p5′C crystallizes in the orthorhombic space group P2 1 2 1 2 1 with a = 8.376(2), b = 16.231(5), c = 18.671(4). CuK ∝ intensity data were collected on a diffractometer in the ω −2θ scan mode. The amount of 1699 out of 2354 reflections having I ≥ 3σ ( 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 (χ 1 = −54°) and that of cytosine is anti (χ 2 = 156°). The 5′ and 2′ and ribose moieties show C2′‐ endo and C3‐ endo mixed puckering just like in A2′p5′A, A2′p5′C, A2′p5U, and dC3′p5′G. Charge neutralization in G2′p5′C is accomplished through protonation of the cytosine base. An important feature of G2′p5′C is the stacking of guanine on ribose 04′ of cytosine similar to that seen in other 2′–5′ dimers. G2′p5′C, unlike its 3′–5′ isomer, does not form a miniature double helix with the Watson‐Crick base‐pairing pattern. Comparison of G2′p5′C with A2′p5′C reveals that they are isostructural. A branched trinucleotide model for the msDNA‐RNA junction has been postulated. © 1994 John Wiley & Sons, Inc.