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There you go: How to get kinetic information from trajectories of single biomolecules? A method based on correlating signal ranges (here for a three-state DNA hairpin with F = folded, I = intermediate, and U = unfolded state) is reported and shows how to get the kinetic scheme and the corresponding rates, even for states with low occupancy or very short lifetime, states which overlap because of noise, and systems with very similar or very different rates.
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Hoffmann et al. (2011) studied this question.
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