Molecular Structure of a DNA Decamer Containing an Anticancer Nucleoside Arabinosylcytosine: Conformational Perturbation by Arabinosylcytosine in B-DNA

Arabinosylcytosine (araC) is an important anticancer drug that has been shown to be misincorporated into DNA double helix. The incorporation of araC into DNA may have significant conformational consequences that could affect the function of DNA. In this paper, we present the high-resolution 3D structure of an araC-containing decamer d[CCAGGC(araC)TGG], as determined by X-ray diffraction analysis, and assess the possible DNA structural perturbation induced by araC. The modified decamer was crystallized in the monoclinic C2 (a = 31.97 Å, b = 25.56 Å, c = 34.62 Å and β = 114.50°) space group, the same as that from d(CCAGGCCTGG) [Heinemann, U., & Alings, C. (1989) J. Mol. Biol. 210, 369]. The structure of the araC-containing decamer was solved by the molecular replacement method and refined by the constrained least-squares refinement procedure to obtain a final R factor of 0.187 using 2349 [>2.0 σ(F)] observed reflections to a resolution of 1.6 Å. The overall conformation resembles that of the canonical decamer DNA structure, but with significant differences in regions close to the araC site. The O2′ hydroxyl groups of the araC residues lie in the major groove of the helix, and they are in close contact with the C5 methyl and C6 H6 atoms of the thymine on the 3′-side. This creates a higher buckle in the araC7-G14 base pair (14°), as compared to that found in the canonical decamer (9°). This may slightly destabilize B-DNA. No direct intramolecular hydrogen bond is formed, in contrast to the situation when araC is incorporated into Z-DNA. In the latter structure, an intramolecular hydrogen bond is formed between O2′ of araC and N2 of the 5′-guanine residues in the deep groove of Z-DNA. On the basis of a model building study, the incorporation of araC into A-DNA or RNA-DNA hybrid structures is found to be disfavored due to the severe steric hindrance resulting from the presence of the O2′ hydroxyl groups. The differential conformational perturbation due to the incorporation of araC between B-DNA and A-DNA (and structurally similar RNA-DNA hybrid) helices may explain the biological roles of araC.