Structure of a B-form DNA/RNA chimera (dC)(rG)d(ATCG) complexed with daunomycin at 1.5 Å resolution (original) (raw)

2003, Acta Crystallographica Section D-biological Crystallography

The crystal structure of a DNA/RNA chimera (dC)(rG)d(ATCG) complexed with the anticancer drug daunomycin has been determined at 1.5 A Ê resolution with R work and R free of 19.7 and 23.3%, respectively, for 2767 re¯ections. The complex crystallizes in space group P4 1 2 1 2, with unit-cell parameters a = b = 28.05, c = 53.16 A Ê , and contains one nucleic acid strand and one daunomycin molecule in the asymmetric unit. To our knowledge, this is the ®rst crystal structure of a DNA/RNA chimera complexed with an intercalating drug. The DNA/RNA chimera adopts the B-form helical conformation, with the 2 H -hydroxyl group in the major groove of the duplex, forming hydrogen bonds to N7 and the anionic phosphate oxygen of its 3 H -side adenine. The present results indicate that the replacement by the ribose sugar in the DNA sequence does not change the geometry and intercalation pattern of daunomycin. A model of B-form RNA has been built based on the present structure. The model indicates that the interactions of the 2 H -hydroxyl groups in the B-form duplex depend on their 3 H -side nucleotides.

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