Hidden Markov model analysis to fluorescence blinking of fluorescently labeled DNA

TL;DR

This study applies hidden Markov models to analyze fluorescence blinking in labeled DNA, revealing exponential ON-duration and log-normal OFF-duration distributions, advancing quantitative understanding of molecular fluorescence dynamics.

Contribution

It introduces a hidden Markov model approach to quantitatively analyze fluorescence blinking, identifying specific probability distributions for ON and OFF states in DNA molecules.

Findings

ON-duration follows an exponential distribution

OFF-duration follows a log-normal distribution

Time-bin dependence affects fluorescence state probabilities

Abstract

We examine quantitatively the transition process from emitting to not-emitting states of fluorescent molecules with a machine learning technique. In a fluorescently labeled DNA, the fluorescence occurs continuously under irradiation, but it often transfers to the not-emitting state corresponding to a charge-separated state. The trajectory of the fluorescence consists of repetitions of light-emitting (ON) and not-emitting (OFF) states, called blinking, and it contains a very large amount of noise due to the several reasons, so in principle, it is difficult to distinguish the ON and OFF states quantitatively. The fluorescence trajectory is a typical stochastic process, and therefore requires advanced time-series data analysis. In the present study, we analyze the fluorescence trajectories using a hidden Markov model, and calculate the probability density of the ON and OFF duration. From the analysis, we found that the ON-duration probability density can be well described by an exponential function, and the OFF-duration probability density can be well described by a log-normal function, which are verified in terms of Kolmogorov-Smirnov test. The time-bin dependence in the fluorescence trajectory on the probability density is carefully analyzed. We also discuss the ON and OFF processes from failure-rate analysis used in life testing of semiconductor devices.