Daunomycin base proton complexation

Base Proton Complexation Shifts The complexation shifts of certain nucleic acid base resonances of poly(dA-dT) on formation of the daunomycin neighbor exclusion complex reflect the shielding contribution due to the anthracycline ring less the contribution from one neighboring base pair which is displaced following intercalation. Thus, the adenosine H-2 resonance remains unperturbed (Figure 27) while the thymidine exchangeable H-3 proton... 

Phosphodiester Linkages The proton noise decoupled lp nmr spectra of the daunomycin poly(dA-dT) complex in 1 M NaCl solution at 67°C have been recorded at 1 antibiotic per 6 base pairs (Nuc/D = 11.8) and 1 antibiotic per A,3 base pairs (Nuc/D = 5.9). Resolved resonances are observed for the complex at both Nuc/D ratios (Figure 32). One of the resonances in the complex exhibits a chemical shift similar to that observed for poly(dA-dT) in 1 M NaCl alone ( 4.1 ppm) at this temperature while the other resonance is shifted downfield by 0.3 ppm in the Nuc/D = 11.8 complex and by 0.45 ppm in the NucD = 5.8 complex (Table XI). The results suggest that daunomycin intercalates at either the dTgdA or dApdT sites, resulting in a downfield shift of the 31p resonance of the corresponding phosphodiester grouping at the intercalation site. 

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. 

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