Daunomycin poly

These phenolic hydroxyls have been observed in the proton NMR spectrum of N-acetyldaunomycin in chloroform solution (83) though they are broadened out due to rapid exchange with solvent in the spectrum of daunomycin in H2O solution. We can therefore compare the H-6 and H-ll ring B hydroxyl chemical shifts of 12.3 and 11.5 ppm for the Nuc/D = 5.9 daunomycin poly(dA-dT) complex in aqueous solution (Figure 25) with the values of 13.86 and 13.15 ppm observed for N-acetyldaunomycin in nonpolar solution (83). 

Figure 25. The 360-MHz correlation proton NMR spectra of the daunomycin poly(dA-dT) complex in /M NaCl, lOmNi cacodylate, lOmM EDTA, 80% HaO— 20% 2H 20. Spectrum A corresponds to the Nuc/D = 11.8 complex, pH 6.0 at 67°C and Spectrum B corresponds to the Nuc/D = 5.9 complex, pH 6.05 at 57°C. The strong resonance corresponds to thymidine H-3 proton of the nucleic acid while the weaker resonances (designated hy asterisks) corresponds to hydroxyl protons at Positions 9 and 11 on Ring B of the anthracycline ring of daunomycin...

Chemical Shifts of Anthracycline Ring B OH Groups at Positions 6 and 11 in the Daunomycin Poly(dA-dT) Complex3... 

Nonexchangeable Proton Spectra Proton spectra of the daunomycin poly(dA-dT) complex in 1 M NaCl, solution have... 

The melting transition of the daunomycin poly(dA-dT) complex can also be monitored at the nucleic acid resonance line widths and the data for the adenosine H-8 resonance are plotted in Figure 28. The resonance is very broad at temperatures below the melting transition of the complexes (dashed curves in Figure 28) indicative of stiffening of the synthetic DNA by the bound anthracycline ring. 

Figure 27. The temperature dependence of the adenosine H-2 resonance (7.1 to 8.1 ppm) for poly(dA-dT) ( ) and the daunomycin poly(dA-dT) complexes, Nuc/D = 50 (A), 25 (O), 9 ( ), and 5 (A.) in IM NaCl, lOrnM cacodylate, 7mM EDTA, HjO solution. The poly(dA-dT) concentration was fixed at I9.3mM in phosphates and the daunomycin concentration was varied to make the different...

Experimental Upfield Anthracycline Complexation Shifts on Formation of The Daunomycin-Poly(dA-dT) Complex... 

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. 

The observation of partially resolved 31p resonances in the daunomycin poly(dA-dT) complex requires that the antibiotic exhibit a preferred specificity for either the pyrimidine(3 -5 ) purine or purine(3 -5 )pyrimidine binding sites. 

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