Base-content dependence of emission enhancements, quantum yields, and lifetimes for cyanine dyes bound to double-strand DNA: Photophysical properties of monomeric and bichromophoric DNA stains

This paper reports fluorescence quantum yield, emission enhancement, and emission lifetime measurements for 10 cyanine dyes complexed to calf thymus DNA (CT-DNA), (dAdT)(10), and (dGdC)(6) duplexes. Six of the dyes are linked bichromophores with four cationic charges per molecule, and four are monomers with two cationic charges per molecule. Emission enhancement is equal to the ratio of emission quantum yields when a dye is bound to double-strand (ds) DNA to that when it is free in solution. Enhancements for these 10 dyes range from 200 to 1800. All of the dyes exhibit either bi- or triexponential emission decay kinetics; reflecting different dye/ds DNA modes of binding, and the average radiative lifetime for the bichromophores bound to ds DNA is 5.1+/-0.8 ns. These results are consistent with expectations that binding-induced restriction of torsion about the central methine bridge is responsible for the large emission enhancements of these dyes. Scrutiny of the lengths of average emission lifetime for these 10 dyes on (dAdT)lo and (dGdC)6 duplexes finds that they do not vary as expected if electron transfer (ET) emission quenching were an important process. Predictions of the relative rates of ET quenching of excited dye emission by the four DNA nucleosides are based on estimates of the free energy of such reactions using redox data for cyanine dye analogues of the DNA-staining dyes. There are also differences in emission quantum yield between dyes with pyridinium and quinolinium structural components when bound to (dAdT)(10) and (dGdC)(6) duplexes. These differences are very distinct for the monomeric dyes where pyridinium dyes have 4-fold greater emission yields on (dAdT)(10) duplexes and quinolinium dyes have 2-fold greater emission yields on (dGdC)(6) duplexes. A 2-fold quantum yield increase on switching from (dAdT)(10) to (dGdC)(6) duplexes is also present for the quinolinium bichromophore, TOTO-1. Very importantly, for this bichromophore and the four monomers the emission quantum yield on CT-DNA matches very well the higher of the short duplex quantum yields. This suggests but does not prove that the pyridinium and quinolinium cyanine dyes selectively associate with AT- and GC-rich regions, respectively, when bound to CT-DNA. For the other five bichromophores studied, there is little difference in emission quantum yield between the two types of short duplexes. Additionally, the emission yields of these bichromophores when bound to CT-DNA do not clearly correspond to either of the short duplex emission yields. Thus, for these dyes there is no clear evidence that they exhibit base-content selectivity with respect to emission yield.