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Intramolecular emission quenching of a photoexcited ruthenium(II) polypyridine by a covalently linked naphthalene diimide (NDI) has been measured in aqueous buffer both without and with calf thymus DNA. The complex consists of a Ru(2,2'-bipyridine)(2)(2,2'-bipyridine-5-carboxamide)(2+) electron donor covalently attached by way of a -CH(2)CH(2)CH(2)- linker to a 1,4,5,8-naphthalene diimide acceptor (Ru-NDI, 1). The NDI portion of the complex intercalates in calf thymus DNA, as indicated by the hypochromism of its optical absorbance bands and observation of an induced circular dichroism spectrum in the same region. Emission quenching in Ru-NDI has been measured relative to a Ru tris-bpy model lacking the NDI moiety by both lifetime and emission quantum yield techniques. Using lifetime averages, the relative emission quenching is, respectively, 99.1% and 97.9% in aqueous buffer solutions without and with DNA. The emission quenching is ascribed to intramolecular electron transfer within the Ru-NDI complex with an estimated driving force (-DeltaG degrees ) of 0.33 eV. In buffer, the emission decays of Ru-NDI alone are fit well with a triexponential model with lifetimes of 0.34 (0.88), 1.99 (0.11), and 12.6 (0.008) ns (relative amplitude). The emission decays of the DNA-intercalated Ru-NDI complex are also fit well with a triexponential model with lifetimes of 0.31 (0.79), 2.00 (0.13), and 11.8 (0.08) ns. Thus, the fractional amplitudes of the lifetimes change upon DNA intercalation of the complex, while the lifetimes themselves remain essentially the same. The average rates of electron transfer in aqueous buffer without and with DNA are, respectively, 1.6 x 10(9) and 6.8 x 10(8) s(-)(1). The striking result of this study is that the overall character of electron transfer quenching in Ru-NDI is very similar whether or not it is bound to DNA. Intercalation of the NDI in DNA apparently has negligible consequences for electron transfer, implying either that the activation energy and electronic coupling in Ru-NDI are largely unaffected by this, at first glance, seemingly significant environmental change or that changes in these parameters on DNA binding cancel fortuitously.

Intramolecular quenching of fluorescence from a cationic porphyrin by a covalently attached ferrocene in both solution and DNA is reported. Two ferrocenyl porphyrins have been prepared, tris(4-N-methylpyridiniumyl), mono(phenyl-OCH2CH2ferrocene)porphyrin, P3Fc, and cis-bis(4-N-methylpyridiniumyl), bis(phenyl-OCH2CH2ferrocene)porphyrin. Binding studies for P3Fc indicate that intercalation of the porphyrin moiety into DNA occurs at low ionic strength (10 mM NaCl); outside binding of the complex is favored at increased ionic strength (100 mM NaCl). The outside binding of P3Fc at high ionic strength is attributed to the hydrophobicity of the molecule, which causes it to undergo salt-induced stacking in aqueous solution. The photophysical properties of P3Fc are examined in MeOH, in phosphate buffer, and in the presence of double-stranded DNA. Efficient quenching of the photoexcited singlet state of the porphyrin by electron transfer from the appended ferrocene is observed in MeOH and buffer solutions with average rate constants of ≥1 × 1010 and 9 × 109 s-1, respectively. When P3Fc is intercalated into DNA, the average rate of photoinduced intramolecular electron transfer is not appreciably reduced (7 × 109 s-1), suggesting that electronic coupling between the D−A pair is strong even under conditions where close contact is restricted. Assuming that for this donor−linker−acceptor complex, in which the porphyrin and ferrocene are separated by an −OCH2CH2− spacer, intercalation of the porphyrin into DNA does not significantly reduce the electronic coupling between the donor and acceptor, the observed subnanosecond electron-transfer rates in and out of DNA show that changes in redox potentials or reorganization energy either compensate one another or have negligible kinetic consequences.

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We describe the synthesis of two novel bis-4H-furo [3,4-b]indoles from indole. Several alternative pathways to these potential DNA bis-intercalator precursors are discussed, and the synthesis of a novel semi-rigid tether is reported.