Analysis of ‘blinking’ or ‘hopping’ single molecule signals with a limited number of transitions

Most single molecule fluorescence signals exhibit two characteristic features: sudden intensity changes (‘blinking’, ‘hopping’) and a limited length (‘bleaching’). I show that the correlation functions of such ‘truncated telegraph signals’ for Poisson processes contain linear segments and oscillatory features, deviating strongly from the expected exponential decay. I find that the slope of the initial linear section of the normalized signal autocorrelation is a robust and reliable statistical estimate for the rate of sudden intensity changes in single molecule fluorescence signals with 4 to 100 transitions per trace, significantly outperforming an exponential fit.