Daunomycin crystal structure

Figure 2 shows the initial equilibrated intercalated state. The DNA sequence is d(GCGCACGTGCGC)2- The intercalated structure s geometry is that of the B-DNA except for the 5th to 7th base pairs (A5 to G7), which stay close to the crystal structure used for the starting conformation, with a root mean square deviation of 3.2 A for all the heavy atoms of those three basepairs. In this sequence, daunomycin is in contact with the strongest binding triplet sequence (A/T)CG [18,19]. Moreover, due to the chosen sequence of the DNA, the intercalation site is flanked by the same sequence of base-pairs in either direction, eliminating any related orientational preference of... 

In all the crystal structures of anthracycline-DNA complexes, the drug molecule is intercalated at the CpG steps. A common feature of the more simple anthracycline antibiotics such as daunomycin and adriamycin is the aglycone aromatic system. 

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