Antibiotic, netropsin • poly

We first describe the NMR parameters for the duplex to strand transition of the synthetic DNA poly(dA-dT) (18) with occasional reference to poly(dA-dU) (24) and poly(dA- brdU) and the corresponding synthetic RNA poly(A-U) (24). This is followed by a comparison of the NMR parameters of the synthetic DNA in the presence of 1 M Na ion and 1 M tetramethylammonium ion in an attempt to investigate the effect of counterion on the conformation and stability of DNA. We next outline structural and dynamical aspects of the complexes of poly(dA-dT) with the mutagen proflavine (25) and the anti-tumor agent daunomycin (26) which intercalate between base pairs and the peptide antibiotic netropsin (27) which binds in the groove of DNA. 

Antibiotic Resonances The protons on the N-methylpyrrole rings of netropsin can be detected in the 1 antibiotic per 5 base pair netropsin poly(dA-dT) complex at 87°C (Figure 41). The proton line widths indicate that the entire complex is intact at this... 

Summary High resolution proton NMR spectroscopy has been utilized to probe the opening of antibiotic-free base pair regions (t 2L 61°C) and those centered about bound netropsin (t 90°C) in the biphasic dissociation of the 1 netropsin per 25 base pair poly(dA-dT) complex in 0.1 M buffer solution with temperature. 

We observe that netropsin binds tightly to DNA and stabilizes 5 base pairs centered about its binding site. The opening rates of the intervening base pair stretches during the dissociation of the antibiotic-free base pair regions in the Nuc/D = 50 complex are slower by an order of magnitude compared to the dissociation rates for the duplex to strand transition of poly(dA-dT) alone in 0.1 M buffer solution. 

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