Specific interaction of netropsin, distamycin-3 and analogs with I.C duplexes: reversion towards the B form of the 2′-deoxy-.2′-deoxy-2′-fluoro- hybrid duplexes upon specific interaction with netropsin, distamydn-3 and analogs

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Abstract
Binding of the B-form specific ligands netropsin and distamycin−3, −4 and −5 has been used to monitor the presence and/or the inducibility of a B-type structure in various poly-inosinic.poly-cytidilic double stranded polymers with deoxyribose, ribose or 2′-deoxy-2′-fluororibose as sugar on either strand. The efficiency of binding was followed by circular dichroism and further evaluated by the increase in melting temperature of the complexes. The efficient binding of netropsin and distamycins to the hybrid polymer (dIfl)n. (dC)n demonstrated that the fluorine carrying strand may undergo a A to B-type transition reflecting a change of the 2′-deoxy-2′-fluororibose from the 3′-endo to the l′-exo or 2′-endo pucker. The less efficient binding of the same ligands to the reverse hybrid (dI)n.(dCfl)n showed that the geometry of the pyrimidine strand is the moat critical for the specific interaction. Taking into account the recent findings about the regular hydration in the minor groove of the B-type dodecamer dCGCGAATTCGCG in solid-state, the different binding modes observed between the different polymers and antibiotics are explained by differences in their possibilities of hydration. Binding of netropsin to a double stranded deoxypolymer is interpreted as a local replacement of water molecules by netropsin in the minor groove hydration network which is typical of the B-form.