BASE-CONTENT DEPENDENCE OF EMISSION ENHANCEMENTS, QUANTUM YIELDS, ANDLIFETIMES FOR CYANINE DYES BOUND TO DOUBLE-STRAND DNA - PHOTOPHYSICALPROPERTIES OF MONOMERIC AND BICHROMOPHORIC DNA STAINS

This paper reports fluorescence quantum yield, emission enhancement, a nd emission lifetime measurements for 10 cyanine dyes complexed to cal f 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. Emissi on 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 sol ution. Enhancements for these 10 dyes range from 200 to 1800. All of t he dyes exhibit either bi- or triexponential emission decay kinetics; reflecting different dye/ds DNA modes of binding, and the average radi ative lifetime for the bichromophores bound to ds DNA is 5.1+/-0.8 ns. These results are consistent with expectations that binding-induced r estriction of torsion about the central methine bridge is responsible for the large emission enhancements of these dyes. Scrutiny of the len gths of average emission lifetime for these 10 dyes on (dAdT)lo and (d GdC)6 duplexes finds that they do not vary as expected if electron tra nsfer (ET) emission quenching were an important process. Predictions o f the relative rates of ET quenching of excited dye emission by the fo ur DNA nucleosides are based on estimates of the free energy of such r eactions using redox data for cyanine dye analogues of the DNA-stainin g dyes. There are also differences in emission quantum yield between d yes with pyridinium and quinolinium structural components when bound t o (dAdT)(10) and (dGdC)(6) duplexes. These differences are very distin ct for the monomeric dyes where pyridinium dyes have 4-fold greater em ission 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 pr esent for the quinolinium bichromophore, TOTO-1. Very importantly, for this bichromophore and the four monomers the emission quantum yield o n CT-DNA matches very well the higher of the short duplex quantum yiel ds. This suggests but does not prove that the pyridinium and quinolini um cyanine dyes selectively associate with AT- and GC-rich regions, re spectively, when bound to CT-DNA. For the other five bichromophores st udied, there is little difference in emission quantum yield between th e two types of short duplexes. Additionally, the emission yields of th ese bichromophores when bound to CT-DNA do not clearly correspond to e ither of the short duplex emission yields. Thus, for these dyes there is no clear evidence that they exhibit base-content selectivity with r espect to emission yield.