Daunomycin geometry

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... 

We have attempted to investigate the daunomycin complex with poly(dA-dT) in order to set constraints on possible overlap geometries in the intercalation complex (26) using methods described in the previous section on the proflavine complex (25). There are nonexchangeable proton markers on ring D and exchangeable proton markers on ring B of the planar portion of the... 

Overlap Geometry at the Intercalation Site We shall attempt to utilize the nucleic acid base and anthracycline ring proton com-plexation shifts to deduce which anthracycline aromatic ring(s) overlap with nearest neighbor base pairs in the daunomycin poly-(dA-dT) intercalation complex. It should be noted that the nonplanarity of ring A in the antibiotic requires that the aromatic portion of the anthracycline chromophore cannot intercalate with its long axis colinear to the direction of the Watson-Crick hydrogen bonds at the intercalation site as was demonstrated for proflavine-nucleic acid complexes. 

Rich s laboratory. We were informed that the sugar residue resides in the minor groove and that the intercalation occurred at dC-dG sites. We recently received the overlap geometry at the intercalation site observed in the daunomycin hexanucleotide crystal (kindly provided by Professor Rich prior to publication) and it is schematically shown below. [6]... 

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