Abstract
We use the minor groove ligand netropsin as a thermodynamic probe of the grooves of parallel DNA. A combination of circular dichroism spectroscopy, temperature-dependent UV spectroscopy, and isothermal titration calorimetry has been employed to characterize the association of netropsin with two sets of DNA 25-mer duplexes: one set contains duplexes with exclusively dA-dT base pairs; the other, duplexes with four dG-dC base pairs in parallel (ps-D1-D2 and ps-D5-D6) and antiparallel (aps-D1-D3 and aps-D5-D7) orientation. Circular dichroism and calorimetric titration curves show overall stoichiometries of 4:1 ([netropsin]:(duplex]) for the netropsin complexes with the antiparallel duplexes and with ps-D1-D2, and 3:1 with ps-D5-D6
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