Structure of a B-form DNA/RNA chimera (dC)(rG)d(ATCG) complexed with daunomycin at 1.5 A resolution.
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 resolution with R(work) and R(free) of 19.7 and 23.3%, respectively, for 2767 reflections. The complex crystallizes in space group P4(1)2(1)2, with unit-cell parameters a = b = 28.05, c = 53.16 A, and contains one nucleic acid strand and one daunomycin molecule in the asymmetric unit. To our knowledge, this is the first 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'-hydroxyl group in the major groove of the duplex, forming hydrogen bonds to N7 and the anionic phosphate oxygen of its 3'-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'-hydroxyl groups in the B-form duplex depend on their 3'-side nucleotides.
Shi
Ke
K
Departments of Chemistry and Biochemistry, The Ohio State University, 200 Johnston Laboratory, 176 West 19th Avenue, Columbus, OH 43210, USA.
Pan
Baocheng
B
Sundaralingam
Muttaiya
M
D000903:Antibiotics, Antineoplastic / Q000737:chemistry; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry*; D003630:Daunorubicin / Q000737:chemistry*; D008956:Models, Chemical; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D010100:Oxygen / Q000737:chemistry; D010710:Phosphates / Q000737:chemistry; D012313:RNA / Q000737:chemistry*; D014867:Water / Q000737:chemistry
D000903:Antibiotics, Antineoplastic; D010710:Phosphates; D014867:Water; D012313:RNA; D004247:DNA; D010100:Oxygen; D003630:Daunorubicin