BINDING OF DAPI ANALOG 2,5-BIS(4-AMIDINOPHENYL)FURAN TO DNA

The binding of 2,5-bis(4-amidinophenyl)furan (APF) to calf thymus DNA, [poly(dA-dT)]2, and [poly(dG-dC)]2 has been studied with flow linear dichroism and circular dichroism spectroscopy. The electronic excited states of the APF chromophore were first characterized using experimen tal and quantum mechanical methods: it is shown that the low-energy ab sorption band (320-400 nm) originates from only a single electronic tr ansition which is polarized along the long axis of the molecule, infor mation that is crucial for the structural interpretation of the linear and circular dichroism spectra of the APF-DNA complexes. By contrast, in the unsymmetric analogue 4',6-diamidino-2-phenylindole (DAPI) two overlapping transitions, with somewhat divergent polarizations, both c ontribute to the first absorption band. Upon binding to DNA the spectr oscopic behavior of APF strongly resembles that of DAPI. The linear di chroism data show that the drug binds to calf thymus DNA and [poly(dA- dT)]2 with an angle of 46-degrees +/- 2-degrees between its symmetry l ong axis and the DNA helix axis, confirming that APF, just like DAPI, is an AT-specific minor-groove binder. Upon binding to [poly(dG-dC)]2, however, the orientation of the long axis is parallel with the plane of the DNA bases, a geometry which excludes binding parallel to the gr ooves but could be consistent with intercalation. However, a short axi s polarized transition is strongly inclined to the base plane and, fur thermore, the persistence length of the polynucleotide is markedly red uced, observations that contradict classical intercalation. The circul ar dichroism spectrum in the low-energy absorption band of APF, upon b inding to [poly(dA-dT)]2, displays a 'two mode' behavior similar to th at of DAPI, which in DAPI has been ascribed to selective activation of either of its two transitions depending on the DNA conformation. Howe ver, in contrast to DAPI, this behavior in APF originates from a singl e electronic transition only. A plausible explanation of the second '' mode'', which could apply to the DAPI case as well, is that it is a re sult of long-range exciton interaction between drug chromophores in th e minor groove.