Single molecule fluorescence fluctuations of the cyanine dyes linked covalently to DNA

The intersystem crossing and isomerization dynamics of free-Cy3, Cy3-ssDNA, free-Cy5 and Cy5-ssDNA are obtained through simple analysis of rapid on/off blinking from single molecule fluorescence intensity time-traces and the fluorescence correlation spectroscopy (FCS). The on- and off-times observed in fluorescence time traces of single cyanine dyes are due to the formation of the triplet state and isomerization, where both the interaction with DNA and long central polymethine chain of cyanine dyes increase the barriers of isomerization, leading to long off-time. The results indicate that the single molecule fluorescence fluctuation together with the resulting second autocorrelation analysis are powerful methods for determining the triplet state and isomerization dynamics, which could be the simple techniques and complementary to other spectroscopic techniques, such as fluorescence decay measurement and laser flash photolysis to study the photophysical processes of complex molecules. Supported by the National Natural Science Foundation of China (Grant Nos. 20773139, 20833008 & 20825314), and State Key Project for Fundamental Research (Grant Nos. 2006CB806000 & 2007CB815200)