Conformation dependent binding of netropsin and distamycin to DNA and DNA model polymers

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Abstract
The binding of the antibiotics netropsin and distamycin A to DNA has been studied by thermal melting, CD and sedimentation analysis. Netropsin binds strongly at antibiotic/nucleotide ratios up to at least 0.05. CD spectra obtained using DNA model polymers reveal that netropsin binds tightly to poly (dA). poly (dT), poly (dA-dT) . poly(dA-dT) and poly (dI-dC)- poly (dI-dC) but poorly, if at all, to poly (dG), poly (dC). Binding curves obtained with calf thymus DNA reveal one netropsin- binding site per 6.0 nucleotides (Ka = 2.9 · 105 M−1); corresponding values for distamycin A are one site per 6.1 nucleotides with Ka = 11.6 · 105 M−1. Binding sites apparently involve predominantly A T-rich sequences whose specific conformation determines their high affinity for the two antibiotics. It is suggested that the binding is stabilized primarily by hydrogen bonding and electrostatic interactions probably in the narrow groove of the DNA helix, but without intercalation. Any local structural deformation of the helix does not involve unwinding greater than approximately 3° per bound antibiotic molecule.